overlaps_strand_bias_to

Get strand bias ratio for overlapping peaks

Bed files are too large for upload but are available upon request; “Table_S5_ext.txt.zip” is available on my Github

#read in all peaks
all <- read.delim("/Users/kathryn/Reprocess_all_paper_datasets/Mol_Cell_resub/Revision_files/Supplementary_Tables/Table_S5_ext.txt", sep = "\t", header = TRUE)

allGR <- makeGRangesFromDataFrame(all,
                                     keep.extra.columns = TRUE,
                                     ignore.strand=FALSE,
                                     seqinfo=NULL,
                                     seqnames.field="chromosome",
                                     start.field="start",
                                     end.field="end",
                                     strand.field="strand",
                                     starts.in.df.are.0based=FALSE)

#get overlapping and disjoint ranges
pos_all <- allGR[allGR@strand=="+"]
neg_all <- allGR[allGR@strand=="-"]

overlapping <- mergeByOverlaps(pos_all, neg_all, minoverlap=10L, ignore.strand = TRUE)
overlapping_r <- c(overlapping@listData$pos_all,overlapping@listData$neg_all)   
overlapping_rf <- GenomicRanges::reduce(overlapping_r, ignore.strand=TRUE) #just giving region with overlap
nonoverlapping <- allGR[allGR %outside% overlapping_rf]

#read in all mapped reads, concatenated by antibody/lysate; data are too large to upload to github; available upon request or raw unprocessed reads can be obtained at GEO accession GSE157168
Dir <- "/Users/kathryn/Reprocess_all_paper_datasets/AaegL5_mapped/cat_beds"
all_reads <- dir(Dir, pattern="*.bed$",full.names = TRUE)
all_reads <- grep("cat", all_reads, value = TRUE)
all_reads_gr <- lapply(all_reads, import, format="BED")
names(all_reads_gr) <- gsub("/Users/kathryn/Reprocess_all_paper_datasets/AaegL5_mapped/cat_beds/", "", all_reads)

#get reads at overlapping peaks
lreads_over_overpeaks <- lapply(all_reads_gr, function(x) mergeByOverlaps(x, overlapping_rf, ignore.strand=TRUE))

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01002203, NIGP01002127, NIGP01000304, NIGP01001514, NIGP01002034, NIGP01001294, NIGP01001039, NIGP01000242, NIGP01000593, NIGP01002289, NIGP01000292, NIGP01002029, NIGP01000294, NIGP01000072, NIGP01002269, NIGP01000033, NIGP01001661, NIGP01000602, NIGP01000433, NIGP01000034, NIGP01001458, NIGP01000697, NIGP01001062, NIGP01000197, NIGP01000541, NIGP01000327, NIGP01001988, NIGP01002253, NIGP01001887, NIGP01000650, NIGP01002196, NIGP01001919, NIGP01000809, NIGP01000504, NIGP01001327, NIGP01002024, NIGP01000398, NIGP01002087, NIGP01001650, NIGP01000361, NIGP01000802, NIGP01000548, NIGP01001757, NIGP01000637, NIGP01001469, NIGP01000780, NIGP01001915, NIGP01001943, NIGP01000920, NIGP01000863, NIGP01000417, NIGP01000039, NIGP01000818, NIGP01000578, NIGP01002242, NIGP01000384, NIGP01000646, NIGP01000962, NIGP01001024, NIGP01000497, NIGP01000916, NIGP01000791, NIGP01000760, NIGP01001028, NIGP01001612, NIGP01002055, NIGP01002044, NIGP01000363, NIGP01002133, NIGP01000123, NIGP01001956, NIGP01000232, NIGP01000142, NIGP01001736, NIGP01000728, NIGP01000290, NIGP01000577, NIGP01001934, NIGP01000747, NIGP01002103, NIGP01002121, NIGP01001977, NIGP01000009, NIGP01001060, NIGP01001893, NIGP01001584, NIGP01001622, NIGP01000148, NIGP01000711, NIGP01000463, NIGP01000450, NIGP01000736, NIGP01000281, NIGP01000031, NIGP01000840, NIGP01001516, NIGP01001961, NIGP01001925, NIGP01001764, NIGP01002054, NIGP01000817, NIGP01001392, NIGP01001058, NIGP01000522, NIGP01000213, NIGP01000464, NIGP01001540, NIGP01000279, NIGP01002191, NIGP01000486, NIGP01001688, NIGP01001950, NIGP01000467, NIGP01000424, NIGP01001542, NIGP01000580, NIGP01000745, NIGP01001781, NIGP01000813, NIGP01000381, NIGP01000620, NIGP01000263, NIGP01000896, NIGP01000046, NIGP01000403, NIGP01000095, NIGP01001704, NIGP01001053, NIGP01000194, NIGP01000568, NIGP01001017, NIGP01002126, NIGP01002031, NIGP01000369, NIGP01001573, NIGP01000291, NIGP01001114, NIGP01000289, NIGP01000476, NIGP01001635, NIGP01001415, NIGP01002077, NIGP01000386, NIGP01002154, NIGP01000190, NIGP01000975, NIGP01000856, NIGP01000269, NIGP01001072, NIGP01000088, NIGP01000583, NIGP01000426, NIGP01000167, NIGP01002163, NIGP01001499, NIGP01000523, NIGP01002202, NIGP01001870, NIGP01001035, NIGP01000709, NIGP01000367, NIGP01000823, NIGP01000103, NIGP01000014, NIGP01002065, NIGP01002169, NIGP01001819, NIGP01001833, NIGP01000969, NIGP01001708, NIGP01001059, NIGP01002283, NIGP01000596, NIGP01001807, NIGP01000375, NIGP01000852, NIGP01000348, NIGP01000344, NIGP01000757, NIGP01000447, NIGP01001805, NIGP01001700, NIGP01000713, NIGP01000069, NIGP01002122, NIGP01000734, NIGP01000047, NIGP01001958, NIGP01001890, NIGP01000453, NIGP01001994, NIGP01000805, NIGP01002180, NIGP01000621, NIGP01000449, NIGP01001989, NIGP01000209, NIGP01002187, NIGP01000156, NIGP01001813, NIGP01002084, NIGP01002039, NIGP01001440, NIGP01001713, NIGP01000005, NIGP01000786, NIGP01000084, NIGP01002189, NIGP01000919, NIGP01001530, NIGP01000107, NIGP01001785, NIGP01000644, NIGP01001014, NIGP01002228, NIGP01000557, NIGP01000329, NIGP01001049, NIGP01002110, NIGP01000246, NIGP01000049, NIGP01002128, NIGP01002129, NIGP01001952, NIGP01000999, NIGP01001074, NIGP01002308, NIGP01002193, NIGP01000053, NIGP01001595, NIGP01001733, NIGP01002288, NIGP01002177, NIGP01001230, NIGP01001838, NIGP01002186, NIGP01000330, NIGP01000617, NIGP01001240, NIGP01001991, NIGP01001046, NIGP01000633, NIGP01000832, NIGP01001821, NIGP01001153, NIGP01000017, NIGP01000654, NIGP01000560, NIGP01001081, NIGP01000652, NIGP01001783, NIGP01000882, NIGP01001067, NIGP01002229, NIGP01000334, NIGP01000616, NIGP01000238, NIGP01000742, NIGP01000543, NIGP01002118, NIGP01000663, NIGP01001178, NIGP01000310, NIGP01001828, NIGP01000649, NIGP01002298, NIGP01000394, NIGP01001743, NIGP01001015, NIGP01000377, NIGP01001677, NIGP01000436, NIGP01001195, NIGP01000261, NIGP01001901, NIGP01002296, NIGP01000674, NIGP01001777, NIGP01000632, NIGP01000546, NIGP01000752, NIGP01000421, NIGP01000089, NIGP01000195, NIGP01000960, NIGP01001996, NIGP01000093, NIGP01001778, NIGP01002241, NIGP01000589, NIGP01000804, NIGP01000325, NIGP01001400, NIGP01001079, NIGP01000353, NIGP01001512, NIGP01000306, NIGP01000400, NIGP01000872, NIGP01000208, NIGP01000527, NIGP01000288, NIGP01001626, NIGP01000951, NIGP01000834, NIGP01000220, NIGP01000679, NIGP01000222, NIGP01002217, NIGP01001681, NIGP01000245, NIGP01000364, NIGP01000419, NIGP01000585, NIGP01000566, NIGP01000695, NIGP01002164, NIGP01002097, NIGP01001636, NIGP01000721, NIGP01000529, NIGP01000410, NIGP01002015, NIGP01001589, NIGP01000655, NIGP01000576, NIGP01001575, NIGP01000264, NIGP01000983, NIGP01001719, NIGP01002007, NIGP01001674, NIGP01000343, NIGP01001841, NIGP01001692, NIGP01000862, NIGP01001978, NIGP01001605, NIGP01002165, NIGP01002049, NIGP01000708, NIGP01000783, NIGP01001825, NIGP01001889, NIGP01001726, NIGP01000143, NIGP01000555, NIGP01000696, NIGP01001623, NIGP01002066, NIGP01000271, NIGP01001932, NIGP01000267, NIGP01002050, NIGP01002222, NIGP01000611, NIGP01000719, NIGP01001655, NIGP01001621, NIGP01000171, NIGP01002258, NIGP01000391, NIGP01001822, NIGP01000698, NIGP01001491, NIGP01000202, NIGP01000492, NIGP01001089, NIGP01000954, NIGP01001830, NIGP01000660, NIGP01001843, NIGP01000801, NIGP01001765, NIGP01000586, NIGP01002075, NIGP01001090, NIGP01000659, NIGP01000795, NIGP01000237, NIGP01001667, NIGP01000799, NIGP01000642, NIGP01000236, NIGP01001585, NIGP01000937, NIGP01001701, NIGP01000884, NIGP01001702, NIGP01000137, NIGP01001544, NIGP01002076, NIGP01002098, NIGP01001643, NIGP01001359, NIGP01001745, NIGP01001532, NIGP01002100, NIGP01001565, NIGP01000998, NIGP01000442, NIGP01001502, NIGP01001332, NIGP01001515, NIGP01001547, NIGP01001878, NIGP01002247, NIGP01000346, NIGP01001063, NIGP01002040, NIGP01000846, NIGP01000966, NIGP01000147, NIGP01001756, NIGP01000873, NIGP01002125, NIGP01000114, NIGP01000841, NIGP01000324, NIGP01000898, NIGP01002306, NIGP01000048, NIGP01001452, NIGP01000412, NIGP01000984, NIGP01000273, NIGP01000145, NIGP01001501, NIGP01000241, NIGP01001981, NIGP01001983, NIGP01001715, NIGP01000672, NIGP01000466, NIGP01000105, NIGP01001656, NIGP01002116, NIGP01000756, NIGP01000122, NIGP01001962, NIGP01001506, NIGP01000755, NIGP01001190, NIGP01001283, NIGP01000889, NIGP01001482, NIGP01000035, NIGP01001871, NIGP01000712, NIGP01000100, NIGP01000989, NIGP01000606, NIGP01000717, NIGP01001619, NIGP01001043, NIGP01001883, NIGP01000758, NIGP01000765, NIGP01001145, NIGP01002162, NIGP01001899, NIGP01002294, NIGP01002112, NIGP01000155, NIGP01001762, NIGP01000342, NIGP01001906, NIGP01000781, NIGP01000141, NIGP01002305, NIGP01002301, NIGP01000833, NIGP01002059, NIGP01000065, NIGP01000420, NIGP01000151, NIGP01000803, NIGP01002279, NIGP01000545, NIGP01000995, NIGP01001766, NIGP01002063, NIGP01002079, NIGP01001792, NIGP01001485, NIGP01000724, NIGP01000883, NIGP01002292, NIGP01000830, NIGP01000910, NIGP01002290, NIGP01001662, NIGP01000974, NIGP01001152, NIGP01000186, NIGP01002102, NIGP01000331, NIGP01000011, NIGP01000927, NIGP01002008, NIGP01002237, NIGP01000691, NIGP01002023, NIGP01001689, NIGP01000499, NIGP01002038, NIGP01001262, NIGP01002092, NIGP01000738, NIGP01001010, NIGP01000079, NIGP01001163, NIGP01000509, NIGP01001110, NIGP01001644, NIGP01001382, NIGP01000073, NIGP01000926, NIGP01001075, NIGP01001800, NIGP01000814, NIGP01000474, NIGP01001596, NIGP01002000, NIGP01002304, NIGP01001794, NIGP01000200, NIGP01000357, NIGP01000435, NIGP01000808, NIGP01001820, NIGP01000615, NIGP01001535, NIGP01002003, NIGP01000605, NIGP01000224, NIGP01002114, NIGP01000296, NIGP01001882, NIGP01001174, NIGP01001823, NIGP01000153, NIGP01000936, NIGP01002053, NIGP01001824, NIGP01002262, NIGP01001173, NIGP01001706, NIGP01001972, NIGP01000913, NIGP01001614, NIGP01000491, NIGP01000284, NIGP01000822, NIGP01002062, NIGP01000601, NIGP01000994, NIGP01002119, NIGP01000934, NIGP01001179, NIGP01001685, NIGP01001418, NIGP01000498, NIGP01000192, NIGP01001742, NIGP01000925, NIGP01000339, NIGP01001130, NIGP01001183, NIGP01001999, NIGP01000314, NIGP01000109, NIGP01001529, NIGP01001594, NIGP01001903, NIGP01000704, NIGP01000931, NIGP01001431, NIGP01001590, NIG

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01002203, NIGP01002127, NIGP01000304, NIGP01001514, NIGP01002034, NIGP01001294, NIGP01001039, NIGP01000242, NIGP01000593, NIGP01002289, NIGP01000292, NIGP01002029, NIGP01000294, NIGP01000072, NIGP01002269, NIGP01000033, NIGP01001661, NIGP01000602, NIGP01000433, NIGP01000034, NIGP01001458, NIGP01000697, NIGP01001062, NIGP01000197, NIGP01000541, NIGP01000327, NIGP01001988, NIGP01002253, NIGP01001887, NIGP01000650, NIGP01002196, NIGP01001919, NIGP01000809, NIGP01000504, NIGP01001327, NIGP01002024, NIGP01000398, NIGP01002087, NIGP01001650, NIGP01000361, NIGP01000802, NIGP01000548, NIGP01001757, NIGP01000637, NIGP01001469, NIGP01000780, NIGP01001915, NIGP01001943, NIGP01000920, NIGP01000863, NIGP01000417, NIGP01000039, NIGP01000818, NIGP01000578, NIGP01002242, NIGP01000384, NIGP01000646, NIGP01000962, NIGP01001024, NIGP01000497, NIGP01000916, NIGP01000791, NIGP01000760, NIGP01001028, NIGP01001612, NIGP01002055, NIGP01002044, NIGP01000363, NIGP01002133, NIGP01000123, NIGP01001956, NIGP01000232, NIGP01000142, NIGP01001736, NIGP01000728, NIGP01000290, NIGP01000577, NIGP01001934, NIGP01000747, NIGP01002103, NIGP01002121, NIGP01001977, NIGP01000009, NIGP01001060, NIGP01001893, NIGP01001584, NIGP01001622, NIGP01000148, NIGP01000711, NIGP01000463, NIGP01000450, NIGP01000736, NIGP01000281, NIGP01000031, NIGP01000840, NIGP01001516, NIGP01001961, NIGP01001925, NIGP01001764, NIGP01002054, NIGP01000817, NIGP01001392, NIGP01001058, NIGP01000522, NIGP01000213, NIGP01000464, NIGP01001540, NIGP01000279, NIGP01002191, NIGP01000486, NIGP01001688, NIGP01001950, NIGP01000467, NIGP01000424, NIGP01001542, NIGP01000580, NIGP01000745, NIGP01001781, NIGP01000813, NIGP01000381, NIGP01000620, NIGP01000263, NIGP01000896, NIGP01000046, NIGP01000403, NIGP01000095, NIGP01001704, NIGP01001053, NIGP01000194, NIGP01000568, NIGP01001017, NIGP01002126, NIGP01002031, NIGP01000369, NIGP01001573, NIGP01000291, NIGP01001114, NIGP01000289, NIGP01000476, NIGP01001635, NIGP01001415, NIGP01002077, NIGP01000386, NIGP01002154, NIGP01000190, NIGP01000975, NIGP01000856, NIGP01000269, NIGP01001072, NIGP01000088, NIGP01000583, NIGP01000426, NIGP01000167, NIGP01002163, NIGP01001499, NIGP01000523, NIGP01002202, NIGP01001870, NIGP01001035, NIGP01000709, NIGP01000367, NIGP01000823, NIGP01000103, NIGP01000014, NIGP01002065, NIGP01002169, NIGP01001819, NIGP01001833, NIGP01000969, NIGP01001708, NIGP01001059, NIGP01002283, NIGP01000596, NIGP01001807, NIGP01000375, NIGP01000852, NIGP01000348, NIGP01000344, NIGP01000757, NIGP01000447, NIGP01001805, NIGP01001700, NIGP01000713, NIGP01000069, NIGP01002122, NIGP01000734, NIGP01000047, NIGP01001958, NIGP01001890, NIGP01000453, NIGP01001994, NIGP01000805, NIGP01002180, NIGP01000621, NIGP01000449, NIGP01001989, NIGP01000209, NIGP01002187, NIGP01000156, NIGP01001813, NIGP01002084, NIGP01002039, NIGP01001440, NIGP01001713, NIGP01000005, NIGP01000786, NIGP01000084, NIGP01002189, NIGP01000919, NIGP01001530, NIGP01000107, NIGP01001785, NIGP01000644, NIGP01001014, NIGP01002228, NIGP01002264, NIGP01000557, NIGP01000329, NIGP01001049, NIGP01002110, NIGP01000246, NIGP01000049, NIGP01002128, NIGP01002129, NIGP01001952, NIGP01000999, NIGP01001074, NIGP01002308, NIGP01002193, NIGP01000053, NIGP01001595, NIGP01001733, NIGP01002288, NIGP01002177, NIGP01001230, NIGP01001838, NIGP01002186, NIGP01000330, NIGP01000617, NIGP01001240, NIGP01001991, NIGP01001046, NIGP01000633, NIGP01000832, NIGP01001821, NIGP01001153, NIGP01000017, NIGP01000654, NIGP01000942, NIGP01000560, NIGP01001081, NIGP01000652, NIGP01001783, NIGP01000055, NIGP01000882, NIGP01001067, NIGP01002229, NIGP01000334, NIGP01000616, NIGP01000238, NIGP01000742, NIGP01000543, NIGP01002118, NIGP01000663, NIGP01001178, NIGP01000310, NIGP01001828, NIGP01000649, NIGP01002298, NIGP01000394, NIGP01001743, NIGP01001015, NIGP01000377, NIGP01001677, NIGP01000436, NIGP01001195, NIGP01000261, NIGP01001901, NIGP01002296, NIGP01000674, NIGP01001777, NIGP01000632, NIGP01000546, NIGP01000752, NIGP01000421, NIGP01000089, NIGP01000195, NIGP01000960, NIGP01001996, NIGP01000093, NIGP01001778, NIGP01002241, NIGP01000589, NIGP01000804, NIGP01000325, NIGP01001400, NIGP01001079, NIGP01001406, NIGP01000353, NIGP01001512, NIGP01000306, NIGP01000400, NIGP01000872, NIGP01000208, NIGP01000527, NIGP01000288, NIGP01001626, NIGP01000951, NIGP01000834, NIGP01000220, NIGP01000679, NIGP01000191, NIGP01000222, NIGP01002217, NIGP01001681, NIGP01001761, NIGP01000245, NIGP01000364, NIGP01000419, NIGP01000585, NIGP01000566, NIGP01000695, NIGP01002164, NIGP01002097, NIGP01001636, NIGP01000721, NIGP01000529, NIGP01000410, NIGP01002015, NIGP01001589, NIGP01000655, NIGP01000576, NIGP01001575, NIGP01000264, NIGP01000983, NIGP01001719, NIGP01002007, NIGP01001674, NIGP01000343, NIGP01001841, NIGP01001692, NIGP01000862, NIGP01001978, NIGP01001605, NIGP01002165, NIGP01002049, NIGP01000708, NIGP01000783, NIGP01001825, NIGP01001889, NIGP01001726, NIGP01000143, NIGP01000555, NIGP01000696, NIGP01001623, NIGP01002066, NIGP01000271, NIGP01001932, NIGP01000267, NIGP01002050, NIGP01002222, NIGP01000611, NIGP01001686, NIGP01000719, NIGP01001655, NIGP01001083, NIGP01001621, NIGP01000171, NIGP01002258, NIGP01000391, NIGP01001822, NIGP01000698, NIGP01001491, NIGP01000202, NIGP01000492, NIGP01001089, NIGP01000954, NIGP01001830, NIGP01000660, NIGP01001843, NIGP01000801, NIGP01001765, NIGP01000586, NIGP01002075, NIGP01001090, NIGP01000659, NIGP01000795, NIGP01000237, NIGP01001667, NIGP01000799, NIGP01000642, NIGP01000236, NIGP01001684, NIGP01001585, NIGP01000937, NIGP01001701, NIGP01000884, NIGP01001702, NIGP01000137, NIGP01001544, NIGP01001555, NIGP01002076, NIGP01002098, NIGP01001643, NIGP01001359, NIGP01001745, NIGP01001532, NIGP01002100, NIGP01001565, NIGP01000998, NIGP01000442, NIGP01001502, NIGP01001332, NIGP01001515, NIGP01001547, NIGP01001878, NIGP01002247, NIGP01000346, NIGP01001063, NIGP01002040, NIGP01000846, NIGP01000966, NIGP01000147, NIGP01001756, NIGP01000873, NIGP01002125, NIGP01000114, NIGP01000841, NIGP01000324, NIGP01000898, NIGP01002306, NIGP01000048, NIGP01001452, NIGP01000412, NIGP01000984, NIGP01000273, NIGP01000145, NIGP01001501, NIGP01000241, NIGP01001981, NIGP01001983, NIGP01001715, NIGP01000672, NIGP01000466, NIGP01000105, NIGP01001656, NIGP01002116, NIGP01000756, NIGP01000122, NIGP01001962, NIGP01001506, NIGP01000755, NIGP01001190, NIGP01001283, NIGP01000889, NIGP01001482, NIGP01000035, NIGP01001871, NIGP01000712, NIGP01000260, NIGP01000100, NIGP01000989, NIGP01000606, NIGP01000717, NIGP01001619, NIGP01002017, NIGP01001043, NIGP01001883, NIGP01000758, NIGP01000765, NIGP01001145, NIGP01002162, NIGP01001899, NIGP01002294, NIGP01002112, NIGP01000155, NIGP01001762, NIGP01000342, NIGP01001906, NIGP01000781, NIGP01000141, NIGP01002305, NIGP01002301, NIGP01000164, NIGP01000833, NIGP01001091, NIGP01002059, NIGP01000065, NIGP01000420, NIGP01000151, NIGP01000803, NIGP01002279, NIGP01000545, NIGP01000995, NIGP01001766, NIGP01002063, NIGP01002079, NIGP01001792, NIGP01001485, NIGP01000724, NIGP01000883, NIGP01002292, NIGP01000830, NIGP01000910, NIGP01002290, NIGP01001662, NIGP01000974, NIGP01001152, NIGP01000186, NIGP01002102, NIGP01000120, NIGP01000331, NIGP01001731, NIGP01000011, NIGP01000927, NIGP01002008, NIGP01002237, NIGP01000691, NIGP01002023, NIGP01001689, NIGP01000499, NIGP01002038, NIGP01001262, NIGP01002092, NIGP01000738, NIGP01000940, NIGP01001010, NIGP01000079, NIGP01001163, NIGP01000509, NIGP01001110, NIGP01001644, NIGP01001382, NIGP01000073, NIGP01001799, NIGP01000926, NIGP01001075, NIGP01001800, NIGP01000814, NIGP01000474, NIGP01001596, NIGP01002000, NIGP01002304, NIGP01001794, NIGP01000200, NIGP01000357, NIGP01000435, NIGP01000808, NIGP01001820, NIGP01000615, NIGP01001535, NIGP01002003, NIGP01000605, NIGP01002136, NIGP01000224, NIGP01002114, NIGP01000296, NIGP01001882, NIGP01001174, NIGP01001823, NIGP01000153, NIGP01000936, NIGP01002053, NIGP01001824, NIGP01002262, NIGP01001173, NIGP01001706, NIGP01001972, NIGP01001872, NIGP01000913, NIGP01001614, NIGP01000491, NIGP01000284, NIGP01000822, NIGP01002062, NIGP01000601, NIGP01000994, NIGP01002119, NIGP01000934, NIG

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01001294, NIGP01000292, NIGP01000197, NIGP01000920, NIGP01002055, NIGP01000232, NIGP01000577, NIGP01002077, NIGP01001700, NIGP01001958, NIGP01001733, NIGP01000420, NIGP01000151, NIGP01001010, NIGP01000200, NIGP01000109, NIGP01001730, NIGP01002190, NIGP01001992, NIGP01000390, NIGP01001465, NIGP01001490, NIGP01001014, NIGP01002228, NIGP01002177, NIGP01001841, NIGP01000241, NIGP01001043, NIGP01002016, NIGP01001419, NIGP01000302, NIGP01001915, NIGP01002242, NIGP01000896, NIGP01000583, NIGP01000801, NIGP01000677, NIGP01000318, NIGP01001124, NIGP01001316, NIGP01000730, NIGP01000347, NIGP01000949, NIGP01002288, NIGP01001783, NIGP01002222, NIGP01001731, NIGP01001850, NIGP01002238, NIGP01002203, NIGP01002127, NIGP01000304, NIGP01001514, NIGP01002034, NIGP01001039, NIGP01000242, NIGP01000593, NIGP01002289, NIGP01002029, NIGP01000294, NIGP01000072, NIGP01002269, NIGP01000033, NIGP01001661, NIGP01000602, NIGP01000433, NIGP01000034, NIGP01000697, NIGP01001062, NIGP01000327, NIGP01001988, NIGP01001887, NIGP01000650, NIGP01002196, NIGP01001919, NIGP01000809, NIGP01000504, NIGP01001327, NIGP01002024, NIGP01000398, NIGP01002087, NIGP01001650, NIGP01000361, NIGP01000802, NIGP01001757, NIGP01001469, NIGP01000780, NIGP01001943, NIGP01000863, NIGP01000417, NIGP01000039, NIGP01000818, NIGP01000646, NIGP01000962, NIGP01001024, NIGP01000497, NIGP01000916, NIGP01000791, NIGP01001028, NIGP01001612, NIGP01002044, NIGP01000363, NIGP01002133, NIGP01000123, NIGP01000142, NIGP01001736, NIGP01000728, NIGP01001934, NIGP01000747, NIGP01002103, NIGP01001977, NIGP01001060, NIGP01001893, NIGP01001622, NIGP01000148, NIGP01000711, NIGP01000463, NIGP01000281, NIGP01000031, NIGP01000840, NIGP01001516, NIGP01001961, NIGP01001925, NIGP01001764, NIGP01001392, NIGP01001058, NIGP01000522, NIGP01000213, NIGP01000464, NIGP01001540, NIGP01000279, NIGP01000486, NIGP01000467, NIGP01001542, NIGP01000580, NIGP01000745, NIGP01000381, NIGP01000620, NIGP01000263, NIGP01000403, NIGP01001704, NIGP01001053, NIGP01000194, NIGP01000568, NIGP01001017, NIGP01002126, NIGP01001573, NIGP01001114, NIGP01000386, NIGP01000975, NIGP01001072, NIGP01000088, NIGP01000167, NIGP01002163, NIGP01001499, NIGP01000523, NIGP01001870, NIGP01000709, NIGP01000823, NIGP01002065, NIGP01002169, NIGP01001819, NIGP01001833, NIGP01001059, NIGP01002283, NIGP01000596, NIGP01000344, NIGP01000757, NIGP01000713, NIGP01000069, NIGP01002122, NIGP01001994, NIGP01002180, NIGP01000621, NIGP01001989, NIGP01000209, NIGP01000156, NIGP01002084, NIGP01002039, NIGP01001440, NIGP01001713, NIGP01000005, NIGP01000084, NIGP01000919, NIGP01000107, NIGP01000644, NIGP01002264, NIGP01000557, NIGP01000329, NIGP01001049, NIGP01002110, NIGP01002128, NIGP01001952, NIGP01000999, NIGP01001074, NIGP01002308, NIGP01002193, NIGP01001838, NIGP01000617, NIGP01001240, NIGP01001991, NIGP01000633, NIGP01000832, NIGP01001821, NIGP01001153, NIGP01000942, NIGP01000652, NIGP01000882, NIGP01001067, NIGP01002229, NIGP01000238, NIGP01001178, NIGP01000310, NIGP01001828, NIGP01000649, NIGP01002298, NIGP01001743, NIGP01000436, NIGP01000261, NIGP01001901, NIGP01000674, NIGP01000546, NIGP01000752, NIGP01000421, NIGP01000089, NIGP01000093, NIGP01001778, NIGP01000325, NIGP01001406, NIGP01000353, NIGP01000527, NIGP01000288, NIGP01001626, NIGP01000951, NIGP01000834, NIGP01000191, NIGP01000222, NIGP01002217, NIGP01001681, NIGP01000419, NIGP01000695, NIGP01002164, NIGP01002097, NIGP01001636, NIGP01000721, NIGP01000529, NIGP01001589, NIGP01000264, NIGP01001719, NIGP01002007, NIGP01000343, NIGP01001692, NIGP01000862, NIGP01001978, NIGP01002049, NIGP01000708, NIGP01001825, NIGP01001889, NIGP01000696, NIGP01000271, NIGP01000267, NIGP01000611, NIGP01001686, NIGP01000719, NIGP01001621, NIGP01002258, NIGP01000391, NIGP01001822, NIGP01001491, NIGP01000492, NIGP01001089, NIGP01000954, NIGP01001830, NIGP01000660, NIGP01000586, NIGP01000659, NIGP01000795, NIGP01001667, NIGP01000799, NIGP01001684, NIGP01001585, NIGP01000937, NIGP01001701, NIGP01000884, NIGP01001544, NIGP01002098, NIGP01001359, NIGP01001532, NIGP01002100, NIGP01001565, NIGP01000442, NIGP01001515, NIGP01001547, NIGP01001063, NIGP01002040, NIGP01000147, NIGP01001756, NIGP01002125, NIGP01000841, NIGP01001452, NIGP01000412, NIGP01001981, NIGP01001983, NIGP01001715, NIGP01000672, NIGP01000105, NIGP01001656, NIGP01002116, NIGP01000756, NIGP01000122, NIGP01001962, NIGP01001506, NIGP01000755, NIGP01001190, NIGP01001283, NIGP01000889, NIGP01001482, NIGP01001871, NIGP01000712, NIGP01000606, NIGP01000717, NIGP01000758, NIGP01002162, NIGP01002294, NIGP01002112, NIGP01000155, NIGP01000833, NIGP01002059, NIGP01000803, NIGP01002279, NIGP01000545, NIGP01001766, NIGP01002063, NIGP01001792, NIGP01001485, NIGP01000724, NIGP01000883, NIGP01002292, NIGP01000830, NIGP01002290, NIGP01000974, NIGP01001152, NIGP01002102, NIGP01000331, NIGP01000011, NIGP01000927, NIGP01002008, NIGP01000691, NIGP01002023, NIGP01001293, NIGP01000499, NIGP01002038, NIGP01001262, NIGP01000738, NIGP01000940, NIGP01000509, NIGP01001110, NIGP01001644, NIGP01001382, NIGP01001799, NIGP01001075, NIGP01000814, NIGP01000474, NIGP01001596, NIGP01002000, NIGP01001794, NIGP01001535, NIGP01002003, NIGP01000605, NIGP01002136, NIGP01000224, NIGP01000296, NIGP01001174, NIGP01001823, NIGP01002262, NIGP01001173, NIGP01001706, NIGP01001872, NIGP01001614, NIGP01000284, NIGP01001179, NIGP01000498, NIGP01000192, NIGP01001742, NIGP01001130, NIGP01001999, NIGP01000314, NIGP01001529, NIGP01001594, NIGP01001832, NIGP01002070, NIGP01000690, NIGP01000671, NIGP01000741, NIGP01000733, NIGP01001789, NIGP01000517, NIGP01000111, NIGP01000029, NIGP01000594, NIGP01001296, NIGP01000455, NIGP01001894, NIGP01002281, NIGP01000625, NIGP01000519, NIGP01000922, NIGP01001559, NIGP01000688, NIGP01001974, NIGP01000964, NIGP01002019, NIGP01000040, NIGP01001373, NIGP01002010, NIGP01001287, NIGP01000506, NIGP01000551, NIGP01000905, NIGP01001709, NIGP01002156, NIGP01001860, NIGP01000071, NIGP01000876, NIGP01001881, NIGP01000702, NIGP01002037, NIGP01000595, NIGP01000396, NIGP01001647, NIGP01002219, NIGP01000448, NIGP01000136, NIGP01000961, NIGP01001496, NIGP01001213, NIGP01001687, NIGP01001092, NIGP01000771, NIGP01000693, NIGP01000918, NIGP01001495, NIGP01001537, NIGP01000559, NIGP01000085, NIGP01001038, NIGP01000762, NIGP01000193, NIGP01000365, NIGP01000368, NIGP01000500, NIGP01000350, NIGP01001788, NIGP01000431, NIGP01001663, NIGP01001840, NIGP01002051, NIGP01000746, NIGP01002036, NIGP01001784, NIGP01000729, NIGP01001910, NIGP01000132, NIGP01001403, NIGP01001963, NIGP01001995, NIGP01000952, NIGP01001070, NIGP01000744, NIGP01000166, NIGP01001861, NIGP01001177, NIGP01001033, NIGP01002124, NIGP01001201, NIGP01000798, NIGP01000930, NIGP01000054, NIGP01002107, NIGP01000395, NIGP01001609, NIGP01002111, NIGP01000235, NIGP01000244, NIGP01000570, NIGP01001922, NIGP01001422, NIGP01002259, NIGP01000668, NIGP01000812, NIGP01002150, NIGP01000631, NIGP01000067, NIGP01001345, NIGP01000874, NIGP01001591, NIGP01000023, NIGP01000684, NIGP01001550, NIGP01001377, NIGP01001143, NIGP01001317, NIGP01000231, NIGP01000090, NIGP01001649, NIGP01001417, NIGP01000705, NIGP01000868, NIGP01000138, NIGP01001141, NIGP01000459, NIGP01001243, NIGP01001597, NIGP01002083, NIGP01000259, NIGP01000163, NIGP01000587, NIGP01001668, NIGP01000494, NIGP01001310, NIGP01000265, NIGP01000275, NIGP01001971, NIGP01000915, NIGP01000196, NIGP01001342, NIGP01001211, NIGP01001355, NIGP01001319, NIGP01001603, NIGP01001151, NIGP01000337, NIGP01001479, NIGP01001160, NIGP01001320, NIGP01001451, NIGP01001203, NIGP01001460, NIGP01001245, NIGP01002291, NIGP01001290, NIGP01001205, NIGP01001304, NIGP01002250, NIGP01000062, NIGP01001187, NIGP01001264, NIGP01000634, NIGP01001337, NIGP01001410, NIGP01001423, NIGP01001891, NIGP01002210, NIGP01001398, NIGP01001251, NIGP01001099, NIGP01002032, NIGP01001362, NIGP01001221, NIGP01001358, NIGP01001344, NIGP01001318, NIGP01001234, NIGP01001303, NIGP01001112, NIGP01001539, NIGP01001405, NIGP01001165, NIGP01001402, NIGP01001420, NIGP01002220, NIGP01001425, NIGP01000037, NIGP01001109, NIGP01001309, NIGP01001434, NIGP01002213, NIGP01001468, NIGP01002299, NIG

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01002196, NIGP01002242, NIGP01000760, NIGP01000424, NIGP01000381, NIGP01001053, NIGP01000386, NIGP01002122, NIGP01002186, NIGP01000017, NIGP01001067, NIGP01001178, NIGP01000546, NIGP01000325, NIGP01000679, NIGP01002097, NIGP01000862, NIGP01000783, NIGP01000143, NIGP01000555, NIGP01001932, NIGP01000391, NIGP01001822, NIGP01000795, NIGP01001643, NIGP01001983, NIGP01000756, NIGP01000889, NIGP01002119, NIGP01000925, NIGP01000876, NIGP01001985, NIGP01000684, NIGP01000705, NIGP01000163, NIGP01002212, NIGP01000915, NIGP01000444, NIGP01002220, NIGP01002225, NIGP01001255, NIGP01002226, NIGP01000255, NIGP01001514, NIGP01002289, NIGP01000292, NIGP01000809, NIGP01000802, NIGP01000780, NIGP01001977, NIGP01000148, NIGP01001764, NIGP01000975, NIGP01000786, NIGP01000238, NIGP01000208, NIGP01001626, NIGP01000834, NIGP01000343, NIGP01000267, NIGP01000660, NIGP01002306, NIGP01000984, NIGP01001906, NIGP01000151, NIGP01000803, NIGP01000545, NIGP01000883, NIGP01000331, NIGP01001974, NIGP01001647, NIGP01001687, NIGP01001495, NIGP01000248, NIGP01000132, NIGP01000701, NIGP01002085, NIGP01000914, NIGP01001151, NIGP01001449, NIGP01001303, NIGP01001888, NIGP01000745, NIGP01001762, NIGP01002038, NIGP01000491, NIGP01001953, NIGP01000338, NIGP01000506, NIGP01001907, NIGP01001487, NIGP01001365, NIGP01002034, NIGP01000072, NIGP01000433, NIGP01001988, NIGP01000650, NIGP01001392, NIGP01000568, NIGP01001017, NIGP01000329, NIGP01000529, NIGP01001575, NIGP01001871, NIGP01002008, NIGP01002203, NIGP01002127, NIGP01000304, NIGP01001294, NIGP01001039, NIGP01000242, NIGP01000593, NIGP01002029, NIGP01000294, NIGP01002269, NIGP01000033, NIGP01001661, NIGP01000034, NIGP01001458, NIGP01000697, NIGP01001062, NIGP01000197, NIGP01000541, NIGP01000327, NIGP01002253, NIGP01001887, NIGP01001919, NIGP01000504, NIGP01002087, NIGP01001650, NIGP01000361, NIGP01000548, NIGP01001757, NIGP01000637, NIGP01001469, NIGP01001943, NIGP01000920, NIGP01000863, NIGP01000417, NIGP01000039, NIGP01000818, NIGP01000578, NIGP01000384, NIGP01000646, NIGP01001024, NIGP01000497, NIGP01000916, NIGP01001028, NIGP01001612, NIGP01002055, NIGP01002044, NIGP01000363, NIGP01002133, NIGP01000123, NIGP01001956, NIGP01000232, NIGP01000142, NIGP01000728, NIGP01000290, NIGP01000577, NIGP01001934, NIGP01000747, NIGP01002121, NIGP01000009, NIGP01001060, NIGP01001893, NIGP01001584, NIGP01001622, NIGP01000711, NIGP01000463, NIGP01000450, NIGP01000736, NIGP01000281, NIGP01000031, NIGP01000840, NIGP01001961, NIGP01001925, NIGP01002054, NIGP01001058, NIGP01000522, NIGP01000213, NIGP01000464, NIGP01000279, NIGP01002191, NIGP01000486, NIGP01001688, NIGP01001950, NIGP01000467, NIGP01001542, NIGP01000580, NIGP01001781, NIGP01000620, NIGP01000896, NIGP01000046, NIGP01000403, NIGP01000095, NIGP01001704, NIGP01000194, NIGP01002126, NIGP01002031, NIGP01000369, NIGP01001573, NIGP01000291, NIGP01001114, NIGP01000476, NIGP01001635, NIGP01001415, NIGP01002077, NIGP01002154, NIGP01000190, NIGP01000856, NIGP01000269, NIGP01001072, NIGP01000088, NIGP01000583, NIGP01000426, NIGP01000167, NIGP01001499, NIGP01002202, NIGP01001035, NIGP01000367, NIGP01000823, NIGP01000103, NIGP01000014, NIGP01002065, NIGP01002169, NIGP01001819, NIGP01001833, NIGP01000969, NIGP01001708, NIGP01001059, NIGP01002283, NIGP01000596, NIGP01001807, NIGP01000375, NIGP01000348, NIGP01000344, NIGP01000757, NIGP01000447, NIGP01001805, NIGP01001700, NIGP01000713, NIGP01000069, NIGP01000047, NIGP01001958, NIGP01001890, NIGP01000453, NIGP01001994, NIGP01000805, NIGP01002180, NIGP01000621, NIGP01000449, NIGP01001989, NIGP01000209, NIGP01000156, NIGP01001813, NIGP01002084, NIGP01002039, NIGP01001440, NIGP01001713, NIGP01000084, NIGP01000919, NIGP01001530, NIGP01000107, NIGP01001785, NIGP01000644, NIGP01001014, NIGP01002228, NIGP01002264, NIGP01000557, NIGP01002110, NIGP01000246, NIGP01000049, NIGP01002129, NIGP01000999, NIGP01001074, NIGP01002308, NIGP01002193, NIGP01000053, NIGP01001595, NIGP01002288, NIGP01002177, NIGP01001230, NIGP01001838, NIGP01000330, NIGP01000617, NIGP01001240, NIGP01001046, NIGP01000832, NIGP01001821, NIGP01001153, NIGP01000654, NIGP01000942, NIGP01001081, NIGP01000652, NIGP01001783, NIGP01000055, NIGP01000882, NIGP01002229, NIGP01000616, NIGP01000742, NIGP01000543, NIGP01002118, NIGP01000663, NIGP01001828, NIGP01000649, NIGP01002298, NIGP01000394, NIGP01001743, NIGP01001015, NIGP01000377, NIGP01001677, NIGP01000436, NIGP01001195, NIGP01000261, NIGP01001901, NIGP01000674, NIGP01001777, NIGP01000632, NIGP01000752, NIGP01000089, NIGP01000195, NIGP01000960, NIGP01001996, NIGP01000093, NIGP01001778, NIGP01002241, NIGP01000589, NIGP01000804, NIGP01001400, NIGP01001406, NIGP01000353, NIGP01001512, NIGP01000306, NIGP01000400, NIGP01000872, NIGP01000527, NIGP01000288, NIGP01000951, NIGP01000220, NIGP01000222, NIGP01001681, NIGP01001761, NIGP01000245, NIGP01000585, NIGP01000566, NIGP01000695, NIGP01002164, NIGP01001636, NIGP01000721, NIGP01000410, NIGP01002015, NIGP01001589, NIGP01000655, NIGP01000576, NIGP01000264, NIGP01000983, NIGP01001719, NIGP01002007, NIGP01001674, NIGP01001841, NIGP01001692, NIGP01001978, NIGP01002165, NIGP01002049, NIGP01000708, NIGP01001825, NIGP01001726, NIGP01000696, NIGP01002066, NIGP01000271, NIGP01002222, NIGP01000611, NIGP01001655, NIGP01001621, NIGP01000171, NIGP01002258, NIGP01000698, NIGP01000202, NIGP01000492, NIGP01000954, NIGP01001830, NIGP01000801, NIGP01001765, NIGP01000586, NIGP01001090, NIGP01000659, NIGP01001667, NIGP01000799, NIGP01000642, NIGP01000236, NIGP01001684, NIGP01001585, NIGP01000884, NIGP01001702, NIGP01000137, NIGP01001555, NIGP01002076, NIGP01002098, NIGP01001745, NIGP01002100, NIGP01001565, NIGP01000998, NIGP01000442, NIGP01001502, NIGP01001332, NIGP01001515, NIGP01001547, NIGP01001878, NIGP01001063, NIGP01002040, NIGP01000966, NIGP01001756, NIGP01000873, NIGP01002125, NIGP01000841, NIGP01000048, NIGP01001452, NIGP01000273, NIGP01000145, NIGP01000241, NIGP01000466, NIGP01001656, NIGP01000122, NIGP01001506, NIGP01000755, NIGP01001283, NIGP01001482, NIGP01000035, NIGP01000712, NIGP01000260, NIGP01000100, NIGP01000989, NIGP01000606, NIGP01000717, NIGP01001619, NIGP01002017, NIGP01001043, NIGP01001883, NIGP01000765, NIGP01001145, NIGP01002162, NIGP01001899, NIGP01002294, NIGP01002112, NIGP01000155, NIGP01000141, NIGP01002305, NIGP01002301, NIGP01000833, NIGP01001091, NIGP01000065, NIGP01000420, NIGP01002279, NIGP01000995, NIGP01001766, NIGP01002079, NIGP01000724, NIGP01000830, NIGP01000910, NIGP01002290, NIGP01001662, NIGP01000974, NIGP01002102, NIGP01000120, NIGP01001731, NIGP01000011, NIGP01000691, NIGP01001689, NIGP01001293, NIGP01000499, NIGP01001262, NIGP01001163, NIGP01000509, NIGP01001110, NIGP01001382, NIGP01000073, NIGP01001075, NIGP01001800, NIGP01002000, NIGP01002304, NIGP01001794, NIGP01000200, NIGP01000808, NIGP01001820, NIGP01000615, NIGP01001535, NIGP01002136, NIGP01000224, NIGP01000296, NIGP01001882, NIGP01000153, NIGP01002053, NIGP01001824, NIGP01002262, NIGP01001173, NIGP01001577, NIGP01001706, NIGP01001972, NIGP01001872, NIGP01000913, NIGP01001614, NIGP01000284, NIGP01000822, NIGP01002062, NIGP01001916, NIGP01001685, NIGP01001418, NIGP01000498, NIGP01000339, NIGP01001130, NIGP01001183, NIGP01001999, NIGP01000314, NIGP01000109, NIGP01001529, NIGP01001594, NIGP01001903, NIGP01000704, NIGP01000931, NIGP01001590, NIGP01001832, NIGP01002070, NIGP01000690, NIGP01001798, NIGP01001032, NIGP01000671, NIGP01000741, NIGP01000733, NIGP01000788, NIGP01000653, NIGP01001229, NIGP01002204, NIGP01000517, NIGP01000385, NIGP01000483, NIGP01000567, NIGP01000594, NIGP01001296, NIGP01001894, NIGP01002281, NIGP01000318, NIGP01001955, NIGP01000685, NIGP01000626, NIGP01000406, NIGP01000519, NIGP01000922, NIGP01001973, NIGP01001559, NIGP01000964, NIGP01002016, NIGP01001373, NIGP01002010, NIGP01001055, NIGP01001054, NIGP01001287, NIGP01001071, NIGP01000496, NIGP01000551, NIGP01000905, NIGP01001709, NIGP01002156, NIGP01001812, NIGP01000569, NIGP01000549, NIGP01001248, NIGP01000071, NIGP01001881, NIGP01000702, NIGP01000297, NIGP01000270, NIGP01002037, NIGP01000595, NIGP01002080, NIGP01001853, NIGP01000396, NIGP01001730, NIGP01002219, NIG

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01000304, NIGP01002034, NIGP01000242, NIGP01000292, NIGP01002029, NIGP01000294, NIGP01000033, NIGP01000602, NIGP01000197, NIGP01001887, NIGP01000650, NIGP01002024, NIGP01000398, NIGP01000802, NIGP01001469, NIGP01000780, NIGP01001915, NIGP01000920, NIGP01000417, NIGP01000818, NIGP01000962, NIGP01001024, NIGP01002044, NIGP01000123, NIGP01000232, NIGP01000577, NIGP01000747, NIGP01002103, NIGP01002121, NIGP01001977, NIGP01001584, NIGP01000711, NIGP01000463, NIGP01000464, NIGP01000467, NIGP01000424, NIGP01000813, NIGP01000046, NIGP01000403, NIGP01000095, NIGP01001053, NIGP01002077, NIGP01002163, NIGP01000709, NIGP01002283, NIGP01000596, NIGP01001807, NIGP01000375, NIGP01000734, NIGP01000453, NIGP01000621, NIGP01002039, NIGP01002228, NIGP01001952, NIGP01002193, NIGP01000053, NIGP01001230, NIGP01000652, NIGP01000649, NIGP01001015, NIGP01000377, NIGP01000421, NIGP01002241, NIGP01000695, NIGP01000721, NIGP01000410, NIGP01001575, NIGP01001719, NIGP01001841, NIGP01001825, NIGP01000143, NIGP01000954, NIGP01001765, NIGP01000795, NIGP01001684, NIGP01001701, NIGP01000147, NIGP01000873, NIGP01000324, NIGP01001452, NIGP01000412, NIGP01000145, NIGP01001501, NIGP01001983, NIGP01001656, NIGP01001962, NIGP01000889, NIGP01001482, NIGP01001883, NIGP01002162, NIGP01001899, NIGP01002294, NIGP01002112, NIGP01000781, NIGP01002305, NIGP01000803, NIGP01000883, NIGP01000910, NIGP01000186, NIGP01002102, NIGP01002237, NIGP01002038, NIGP01001262, NIGP01000509, NIGP01000814, NIGP01000200, NIGP01000822, NIGP01001431, NIGP01001789, NIGP01002142, NIGP01001055, NIGP01001287, NIGP01000569, NIGP01000297, NIGP01000270, NIGP01001730, NIGP01001931, NIGP01000787, NIGP01000693, NIGP01001228, NIGP01000479, NIGP01001926, NIGP01000762, NIGP01001663, NIGP01002036, NIGP01001910, NIGP01000730, NIGP01001070, NIGP01002138, NIGP01000461, NIGP01001609, NIGP01000860, NIGP01001422, NIGP01000668, NIGP01000592, NIGP01000631, NIGP01001345, NIGP01001850, NIGP01000074, NIGP01000259, NIGP01000434, NIGP01000265, NIGP01001151, NIGP01001160, NIGP01001460, NIGP01001187, NIGP01000869, NIGP01001295, NIGP01001221, NIGP01001249, NIGP01001102, NIGP01002220, NIGP01001425, NIGP01001886, NIGP01001412, NIGP01001271, NIGP01001486, NIGP01001333, NIGP01000255, NIGP01002127, NIGP01001039, NIGP01000593, NIGP01002269, NIGP01001661, NIGP01000034, NIGP01000541, NIGP01002253, NIGP01001919, NIGP01002087, NIGP01000384, NIGP01000009, NIGP01001060, NIGP01001622, NIGP01000736, NIGP01002054, NIGP01001392, NIGP01000896, NIGP01000194, NIGP01002126, NIGP01000291, NIGP01000088, NIGP01002202, NIGP01001805, NIGP01000047, NIGP01000156, NIGP01002264, NIGP01000557, NIGP01001240, NIGP01000017, NIGP01000543, NIGP01002118, NIGP01000310, NIGP01001677, NIGP01000674, NIGP01000589, NIGP01000208, NIGP01001626, NIGP01001681, NIGP01001692, NIGP01001889, NIGP01000271, NIGP01001932, NIGP01002222, NIGP01001686, NIGP01001083, NIGP01001491, NIGP01001585, NIGP01000884, NIGP01001702, NIGP01001544, NIGP01001547, NIGP01001756, NIGP01002125, NIGP01000273, NIGP01001715, NIGP01000756, NIGP01000260, NIGP01000717, NIGP01000765, NIGP01000164, NIGP01000830, NIGP01000011, NIGP01002023, NIGP01001689, NIGP01001293, NIGP01002053, NIGP01001972, NIGP01000913, NIGP01000994, NIGP01000741, NIGP01000733, NIGP01001006, NIGP01000519, NIGP01000961, NIGP01000368, NIGP01001912, NIGP01000027, NIGP01001299, NIGP01002124, NIGP01002105, NIGP01002132, NIGP01000754, NIGP01002150, NIGP01000684, NIGP01001668, NIGP01001321, NIGP01001205, NIGP01002250, NIGP01001449, NIGP01001286, NIGP01001131, NIGP01001300, NIGP01002197, NIGP01001494, NIGP01002225, NIGP01001372, NIGP01001428, NIGP01000050, NIGP01001490, NIGP01001346, NIGP01001244, NIGP01002074, NIGP01000777, NIGP01001514, NIGP01001294, NIGP01002289, NIGP01000072, NIGP01000433, NIGP01002196, NIGP01001757, NIGP01000863, NIGP01002242, NIGP01000497, NIGP01000760, NIGP01000363, NIGP01002133, NIGP01001736, NIGP01000840, NIGP01001925, NIGP01001058, NIGP01001688, NIGP01000745, NIGP01001573, NIGP01001114, NIGP01001415, NIGP01001870, NIGP01000823, NIGP01000014, NIGP01001833, NIGP01001708, NIGP01000344, NIGP01000757, NIGP01001958, NIGP01001994, NIGP01000786, NIGP01002129, NIGP01002308, NIGP01001733, NIGP01000330, NIGP01000617, NIGP01000055, NIGP01000882, NIGP01002229, NIGP01001178, NIGP01000306, NIGP01000527, NIGP01002217, NIGP01000245, NIGP01002097, NIGP01001636, NIGP01000529, NIGP01000783, NIGP01000555, NIGP01002258, NIGP01001089, NIGP01001830, NIGP01000660, NIGP01000237, NIGP01000799, NIGP01000236, NIGP01000137, NIGP01001745, NIGP01000846, NIGP01001506, NIGP01001871, NIGP01000155, NIGP01001762, NIGP01000342, NIGP01000141, NIGP01002301, NIGP01000151, NIGP01001766, NIGP01002063, NIGP01002079, NIGP01001485, NIGP01000499, NIGP01002092, NIGP01001010, NIGP01001799, NIGP01001075, NIGP01001800, NIGP01001535, NIGP01000936, NIGP01001173, NIGP01001872, NIGP01001130, NIGP01001590, NIGP01000690, NIGP01000671, NIGP01000788, NIGP01000625, NIGP01000496, NIGP01001709, NIGP01000549, NIGP01001248, NIGP01002037, NIGP01001647, NIGP01001274, NIGP01001001, NIGP01002271, NIGP01001092, NIGP01000773, NIGP01001124, NIGP01000193, NIGP01000370, NIGP01000746, NIGP01001096, NIGP01001037, NIGP01001784, NIGP01001403, NIGP01000540, NIGP01002060, NIGP01001177, NIGP01001723, NIGP01001236, NIGP01000798, NIGP01001631, NIGP01002259, NIGP01001985, NIGP01000231, NIGP01000090, NIGP01001417, NIGP01000900, NIGP01000458, NIGP01001113, NIGP01000915, NIGP01001603, NIGP01001397, NIGP01000444, NIGP01001112, NIGP01002211, NIGP01001948, NIGP01001125, NIGP01001465, NIGP01000503, NIGP01001851, NIGP01001473, NIGP01001246, NIGP01001167, NIGP01000903, NIGP01002246, NIGP01002266, NIGP01000753, NIGP01001608, NIGP01000026, NIGP01000542, NIGP01000722, NIGP01002282, NIGP01001458, NIGP01000916, NIGP01001956, NIGP01000142, NIGP01000728, NIGP01000148, NIGP01000450, NIGP01001516, NIGP01001961, NIGP01001764, NIGP01001540, NIGP01000279, NIGP01000620, NIGP01000263, NIGP01000568, NIGP01000369, NIGP01000856, NIGP01001700, NIGP01002122, NIGP01000805, NIGP01000209, NIGP01001713, NIGP01002189, NIGP01001014, NIGP01002128, NIGP01001595, NIGP01002288, NIGP01001821, NIGP01001081, NIGP01001828, NIGP01001901, NIGP01000752, NIGP01000960, NIGP01001778, NIGP01001406, NIGP01000353, NIGP01000872, NIGP01002015, NIGP01000983, NIGP01001674, NIGP01000708, NIGP01001623, NIGP01000611, NIGP01001843, NIGP01000801, NIGP01001643, NIGP01001332, NIGP01001878, NIGP01002306, NIGP01001981, NIGP01001190, NIGP01001283, NIGP01001043, NIGP01001091, NIGP01000974, NIGP01002008, NIGP01001110, NIGP01001644, NIGP01001382, NIGP01002000, NIGP01000357, NIGP01000605, NIGP01001882, NIGP01002119, NIGP01001685, NIGP01000931, NIGP01000517, NIGP01000385, NIGP01000922, NIGP01000687, NIGP01000688, NIGP01000595, NIGP01002080, NIGP01000686, NIGP01000669, NIGP01000199, NIGP01000320, NIGP01001305, NIGP01000462, NIGP01000559, NIGP01000776, NIGP01001840, NIGP01001050, NIGP01001095, NIGP01002272, NIGP01001861, NIGP01001033, NIGP01001732, NIGP01001238, NIGP01000054, NIGP01002085, NIGP01002111, NIGP01000689, NIGP01001042, NIGP01000235, NIGP01001356, NIGP01000067, NIGP01001377, NIGP01001141, NIGP01000957, NIGP01000890, NIGP01000163, NIGP01002212, NIGP01001479, NIGP01001290, NIGP01001218, NIGP01000062, NIGP01000390, NIGP01001891, NIGP01001362, NIGP01001391, NIGP01001402, NIGP01001171, NIGP01001468, NIGP01001888, NIGP01001127, NIGP01001225, NIGP01000243, NIGP01001207, NIGP01000678, NIGP01000323, NIGP01000828, NIGP01000857, NIGP01001869, NIGP01002203, NIGP01000697, NIGP01001062, NIGP01000327, NIGP01001988, NIGP01000809, NIGP01001650, NIGP01000361, NIGP01000548, NIGP01000637, NIGP01001943, NIGP01000039, NIGP01000578, NIGP01000646, NIGP01000791, NIGP01001028, NIGP01001612, NIGP01000290, NIGP01001934, NIGP01001893, NIGP01000281, NIGP01000817, NIGP01000213, NIGP01000486, NIGP01001950, NIGP01001542, NIGP01000580, NIGP01001781, NIGP01000381, NIGP01001704, NIGP01001635, NIGP01002154, NIGP01001072, NIGP01000426, NIGP01000167, NIGP01001499, NIGP01000523, NIGP01001035, NIGP01000103, NIGP01002065, NIGP01002169, NIGP01001819, NIGP01000852, NIGP01000447, NIGP01000713, NIGP01000069, NIGP01000449, NIG

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01002203, NIGP01002127, NIGP01000304, NIGP01001039, NIGP01000242, NIGP01000292, NIGP01002029, NIGP01000294, NIGP01000033, NIGP01000602, NIGP01001062, NIGP01000197, NIGP01000541, NIGP01000327, NIGP01000650, NIGP01001327, NIGP01000398, NIGP01000361, NIGP01000802, NIGP01001469, NIGP01000780, NIGP01001915, NIGP01001943, NIGP01000920, NIGP01000417, NIGP01002242, NIGP01000646, NIGP01000962, NIGP01000497, NIGP01000916, NIGP01001612, NIGP01002044, NIGP01000142, NIGP01000577, NIGP01001934, NIGP01000747, NIGP01002103, NIGP01000009, NIGP01001060, NIGP01000031, NIGP01000840, NIGP01000522, NIGP01000279, NIGP01002191, NIGP01001688, NIGP01001542, NIGP01000745, NIGP01000813, NIGP01000403, NIGP01001053, NIGP01002031, NIGP01001573, NIGP01000289, NIGP01001635, NIGP01002077, NIGP01002154, NIGP01000975, NIGP01000167, NIGP01002163, NIGP01000523, NIGP01001870, NIGP01001035, NIGP01000709, NIGP01000367, NIGP01000823, NIGP01000103, NIGP01000014, NIGP01002065, NIGP01001833, NIGP01002283, NIGP01000375, NIGP01000852, NIGP01000447, NIGP01001700, NIGP01000734, NIGP01001890, NIGP01002187, NIGP01000156, NIGP01001813, NIGP01002084, NIGP01001440, NIGP01000919, NIGP01001530, NIGP01001014, NIGP01002264, NIGP01000246, NIGP01002128, NIGP01001952, NIGP01000999, NIGP01002193, NIGP01002186, NIGP01000330, NIGP01001240, NIGP01001046, NIGP01001081, NIGP01000652, NIGP01001783, NIGP01000882, NIGP01002229, NIGP01001828, NIGP01000649, NIGP01002298, NIGP01000394, NIGP01001743, NIGP01001015, NIGP01001677, NIGP01001195, NIGP01001777, NIGP01000546, NIGP01000752, NIGP01000421, NIGP01000089, NIGP01000960, NIGP01000589, NIGP01001400, NIGP01000721, NIGP01001589, NIGP01000576, NIGP01001575, NIGP01000983, NIGP01001719, NIGP01000343, NIGP01001841, NIGP01000862, NIGP01002049, NIGP01000708, NIGP01000783, NIGP01001825, NIGP01001889, NIGP01001726, NIGP01000143, NIGP01000696, NIGP01002066, NIGP01000271, NIGP01001932, NIGP01000719, NIGP01001655, NIGP01002258, NIGP01000202, NIGP01001089, NIGP01000954, NIGP01001843, NIGP01000801, NIGP01000659, NIGP01000642, NIGP01000236, NIGP01001684, NIGP01001585, NIGP01001702, NIGP01001555, NIGP01002076, NIGP01002098, NIGP01001359, NIGP01001565, NIGP01001502, NIGP01001515, NIGP01001547, NIGP01002247, NIGP01002040, NIGP01000966, NIGP01001756, NIGP01000114, NIGP01000324, NIGP01000048, NIGP01000412, NIGP01000145, NIGP01001501, NIGP01001715, NIGP01000105, NIGP01001962, NIGP01001482, NIGP01001871, NIGP01000712, NIGP01000100, NIGP01000989, NIGP01001883, NIGP01000765, NIGP01002162, NIGP01001899, NIGP01000155, NIGP01001906, NIGP01000065, NIGP01000420, NIGP01000151, NIGP01000545, NIGP01001766, NIGP01002063, NIGP01000724, NIGP01000883, NIGP01000830, NIGP01000910, NIGP01002290, NIGP01002008, NIGP01000691, NIGP01000073, NIGP01002000, NIGP01000357, NIGP01000615, NIGP01001535, NIGP01002114, NIGP01000296, NIGP01000153, NIGP01001173, NIGP01001577, NIGP01000913, NIGP01000491, NIGP01000601, NIGP01002119, NIGP01000934, NIGP01001179, NIGP01000498, NIGP01000339, NIGP01001130, NIGP01001594, NIGP01000677, NIGP01002070, NIGP01000690, NIGP01000733, NIGP01001789, NIGP01001229, NIGP01000517, NIGP01000111, NIGP01002142, NIGP01001894, NIGP01000685, NIGP01000922, NIGP01001287, NIGP01001348, NIGP01000897, NIGP01000488, NIGP01002156, NIGP01000569, NIGP01000549, NIGP01001248, NIGP01000071, NIGP01000876, NIGP01000571, NIGP01001881, NIGP01000297, NIGP01000270, NIGP01000595, NIGP01000396, NIGP01001931, NIGP01002219, NIGP01002190, NIGP01000448, NIGP01000136, NIGP01000538, NIGP01001939, NIGP01000624, NIGP01001124, NIGP01000762, NIGP01000193, NIGP01000365, NIGP01001913, NIGP01000368, NIGP01000776, NIGP01001788, NIGP01000746, NIGP01002036, NIGP01000248, NIGP01001784, NIGP01002214, NIGP01000132, NIGP01000389, NIGP01000701, NIGP01000935, NIGP01001995, NIGP01000952, NIGP01002060, NIGP01001070, NIGP01001861, NIGP01001033, NIGP01000347, NIGP01002124, NIGP01002274, NIGP01000054, NIGP01001631, NIGP01002138, NIGP01000461, NIGP01000860, NIGP01000235, NIGP01000244, NIGP01001922, NIGP01002132, NIGP01001356, NIGP01000812, NIGP01002150, NIGP01000592, NIGP01001345, NIGP01000287, NIGP01001850, NIGP01002198, NIGP01000115, NIGP01001591, NIGP01000684, NIGP01002171, NIGP01000459, NIGP01002206, NIGP01001357, NIGP01000458, NIGP01000163, NIGP01000587, NIGP01002205, NIGP01000494, NIGP01001310, NIGP01001489, NIGP01000915, NIGP01000949, NIGP01001211, NIGP01001355, NIGP01001321, NIGP01001603, NIGP01000337, NIGP01001256, NIGP01001129, NIGP01001187, NIGP01000634, NIGP01000869, NIGP01002210, NIGP01001295, NIGP01001397, NIGP01001358, NIGP01001449, NIGP01001318, NIGP01001483, NIGP01001112, NIGP01001948, NIGP01001249, NIGP01001405, NIGP01001102, NIGP01001191, NIGP01002220, NIGP01001269, NIGP01001263, NIGP01001309, NIGP01001888, NIGP01001271, NIGP01001494, NIGP01001600, NIGP01001486, NIGP01001334, NIGP01000503, NIGP01001475, NIGP01000050, NIGP01002277, NIGP01001754, NIGP01001116, NIGP01000303, NIGP01001207, NIGP01001441, NIGP01002246, NIGP01001182, NIGP01000454, NIGP01001094, NIGP01002183, NIGP01002184, NIGP01000307, NIGP01001849, NIGP01001514, NIGP01002034, NIGP01001294, NIGP01000593, NIGP01000072, NIGP01002269, NIGP01001661, NIGP01000433, NIGP01000034, NIGP01000697, NIGP01001988, NIGP01000809, NIGP01002087, NIGP01001650, NIGP01001757, NIGP01000863, NIGP01000818, NIGP01000578, NIGP01001024, NIGP01000791, NIGP01000760, NIGP01000363, NIGP01002133, NIGP01000123, NIGP01000232, NIGP01002121, NIGP01001977, NIGP01001893, NIGP01001584, NIGP01001622, NIGP01000711, NIGP01000463, NIGP01000450, NIGP01001516, NIGP01001961, NIGP01001925, NIGP01001764, NIGP01002054, NIGP01001392, NIGP01001058, NIGP01000213, NIGP01000467, NIGP01000424, NIGP01000580, NIGP01000263, NIGP01000896, NIGP01000095, NIGP01000568, NIGP01001017, NIGP01002126, NIGP01000369, NIGP01000476, NIGP01000386, NIGP01000856, NIGP01000269, NIGP01001072, NIGP01000583, NIGP01000426, NIGP01000969, NIGP01001059, NIGP01001807, NIGP01000348, NIGP01000757, NIGP01001805, NIGP01001958, NIGP01001994, NIGP01002180, NIGP01000449, NIGP01000786, NIGP01000084, NIGP01000049, NIGP01002129, NIGP01002308, NIGP01000053, NIGP01002177, NIGP01000617, NIGP01001153, NIGP01000942, NIGP01000055, NIGP01001067, NIGP01000238, NIGP01001178, NIGP01000377, NIGP01001901, NIGP01002296, NIGP01000674, NIGP01000195, NIGP01002241, NIGP01000325, NIGP01001079, NIGP01001406, NIGP01000353, NIGP01001512, NIGP01000208, NIGP01000527, NIGP01000288, NIGP01001626, NIGP01000834, NIGP01000222, NIGP01001681, NIGP01000364, NIGP01000585, NIGP01000566, NIGP01000695, NIGP01001636, NIGP01000529, NIGP01000410, NIGP01000655, NIGP01001692, NIGP01002165, NIGP01000555, NIGP01001623, NIGP01002050, NIGP01001686, NIGP01000492, NIGP01001830, NIGP01000660, NIGP01000586, NIGP01000795, NIGP01001667, NIGP01000137, NIGP01002100, NIGP01000998, NIGP01000442, NIGP01001878, NIGP01000147, NIGP01002125, NIGP01000841, NIGP01000241, NIGP01001983, NIGP01000466, NIGP01001656, NIGP01000756, NIGP01001190, NIGP01002112, NIGP01000781, NIGP01000141, NIGP01001091, NIGP01002059, NIGP01000803, NIGP01001792, NIGP01000974, NIGP01000186, NIGP01002102, NIGP01000120, NIGP01002038, NIGP01001110, NIGP01001794, NIGP01000605, NIGP01001174, NIGP01000936, NIGP01002053, NIGP01001824, NIGP01001706, NIGP01000284, NIGP01000822, NIGP01000994, NIGP01001916, NIGP01000925, NIGP01001183, NIGP01001529, NIGP01000704, NIGP01000671, NIGP01000741, NIGP01000338, NIGP01000653, NIGP01001013, NIGP01000029, NIGP01000385, NIGP01000483, NIGP01000594, NIGP01001296, NIGP01002281, NIGP01000625, NIGP01000519, NIGP01000687, NIGP01001973, NIGP01001559, NIGP01002016, NIGP01001055, NIGP01000551, NIGP01000702, NIGP01001853, NIGP01000787, NIGP01002271, NIGP01001228, NIGP01001495, NIGP01001305, NIGP01001038, NIGP01001718, NIGP01000431, NIGP01001840, NIGP01002051, NIGP01000973, NIGP01000540, NIGP01001095, NIGP01001177, NIGP01001732, NIGP01000798, NIGP01000930, NIGP01001992, NIGP01002107, NIGP01000395, NIGP01002148, NIGP01002085, NIGP01001422, NIGP01002259, NIGP01000754, NIGP01000502, NIGP01000874, NIGP01000023, NIGP01001550, NIGP01001317, NIGP01001417, NIGP01000891, NIGP01000868, NIGP01001141, NIGP01001243, NIGP01001597, NIGP01002083, NIG

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01002203, NIGP01001039, NIGP01000072, NIGP01002269, NIGP01000602, NIGP01000197, NIGP01002253, NIGP01001887, NIGP01000650, NIGP01002087, NIGP01000361, NIGP01001956, NIGP01000281, NIGP01001781, NIGP01000813, NIGP01002126, NIGP01000190, NIGP01000269, NIGP01000709, NIGP01001819, NIGP01000969, NIGP01000047, NIGP01001014, NIGP01001952, NIGP01001821, NIGP01001081, NIGP01000527, NIGP01000679, NIGP01000222, NIGP01002097, NIGP01001719, NIGP01000611, NIGP01002258, NIGP01000998, NIGP01001756, NIGP01001981, NIGP01001983, NIGP01000672, NIGP01001656, NIGP01001283, NIGP01001871, NIGP01000342, NIGP01001906, NIGP01000724, NIGP01000830, NIGP01000910, NIGP01000153, NIGP01000925, NIGP01001184, NIGP01001955, NIGP01001287, NIGP01000897, NIGP01000071, NIGP01000132, NIGP01001070, NIGP01001861, NIGP01001356, NIGP01000592, NIGP01001227, NIGP01002185, NIGP01001172, NIGP01001355, NIGP01001451, NIGP01001304, NIGP01001162, NIGP01001112, NIGP01001102, NIGP01001309, NIGP01001453, NIGP01001888, NIGP01001284, NIGP01001200, NIGP01001166, NIGP01000911, NIGP01000304, NIGP01000294, NIGP01000033, NIGP01000433, NIGP01001458, NIGP01000697, NIGP01000398, NIGP01001757, NIGP01000863, NIGP01000962, NIGP01000497, NIGP01000363, NIGP01001934, NIGP01000747, NIGP01000009, NIGP01000450, NIGP01001058, NIGP01000464, NIGP01000279, NIGP01000467, NIGP01000263, NIGP01002065, NIGP01000209, NIGP01002187, NIGP01002039, NIGP01001713, NIGP01000633, NIGP01000017, NIGP01001195, NIGP01000752, NIGP01000089, NIGP01000834, NIGP01000721, NIGP01000708, NIGP01001623, NIGP01002100, NIGP01002059, NIGP01000803, NIGP01000995, NIGP01002038, NIGP01000357, NIGP01002136, NIGP01001789, NIGP01001006, NIGP01000687, NIGP01001973, NIGP01001974, NIGP01002019, NIGP01001632, NIGP01000669, NIGP01000762, NIGP01000744, NIGP01001261, NIGP01000798, NIGP01000860, NIGP01001670, NIGP01000259, NIGP01001256, NIGP01001187, NIGP01001443, NIGP01001384, NIGP01001266, NIGP01002127, NIGP01002289, NIGP01000292, NIGP01001661, NIGP01000034, NIGP01001062, NIGP01001650, NIGP01000802, NIGP01000780, NIGP01001943, NIGP01000818, NIGP01002242, NIGP01002055, NIGP01000142, NIGP01000290, NIGP01002103, NIGP01001961, NIGP01001764, NIGP01001053, NIGP01001017, NIGP01001573, NIGP01000291, NIGP01001114, NIGP01000476, NIGP01000856, NIGP01000426, NIGP01000823, NIGP01000069, NIGP01002122, NIGP01000453, NIGP01000156, NIGP01000919, NIGP01000644, NIGP01002264, NIGP01001049, NIGP01000246, NIGP01001074, NIGP01000053, NIGP01001046, NIGP01001828, NIGP01000649, NIGP01000674, NIGP01001777, NIGP01000195, NIGP01000353, NIGP01001512, NIGP01000695, NIGP01000529, NIGP01000576, NIGP01001575, NIGP01000343, NIGP01001841, NIGP01000555, NIGP01001655, NIGP01000391, NIGP01001585, NIGP01001502, NIGP01001063, NIGP01000466, NIGP01000105, NIGP01000122, NIGP01001506, NIGP01000712, NIGP01002294, NIGP01000545, NIGP01001794, NIGP01000435, NIGP01000808, NIGP01001535, NIGP01000296, NIGP01001685, NIGP01000339, NIGP01000733, NIGP01000517, NIGP01001894, NIGP01000519, NIGP01002010, NIGP01001055, NIGP01001860, NIGP01000549, NIGP01000297, NIGP01002080, NIGP01001687, NIGP01000624, NIGP01001038, NIGP01000365, NIGP01001096, NIGP01000729, NIGP01000732, NIGP01000372, NIGP01000395, NIGP01002117, NIGP01001850, NIGP01000023, NIGP01000231, NIGP01002171, NIGP01002212, NIGP01000265, NIGP01000915, NIGP01001211, NIGP01001603, NIGP01001129, NIGP01001203, NIGP01000634, NIGP01001375, NIGP01002032, NIGP01001358, NIGP01001318, NIGP01001402, NIGP01002220, NIGP01001365, NIGP01001450, NIGP01001372, NIGP01001387, NIGP01002239, NIGP01000753, NIGP01001834, NIGP01001885, NIGP01002034, NIGP01000242, NIGP01000541, NIGP01001988, NIGP01002196, NIGP01000504, NIGP01001469, NIGP01000417, NIGP01000039, NIGP01000578, NIGP01000384, NIGP01000791, NIGP01001028, NIGP01000577, NIGP01000711, NIGP01000736, NIGP01001516, NIGP01001925, NIGP01000213, NIGP01000095, NIGP01000194, NIGP01002031, NIGP01000369, NIGP01002077, NIGP01000386, NIGP01000523, NIGP01001059, NIGP01000348, NIGP01000049, NIGP01002308, NIGP01002193, NIGP01000394, NIGP01000377, NIGP01000436, NIGP01000951, NIGP01002217, NIGP01002164, NIGP01001636, NIGP01002007, NIGP01002222, NIGP01001090, NIGP01001667, NIGP01000236, NIGP01001684, NIGP01000137, NIGP01001544, NIGP01002098, NIGP01002247, NIGP01002125, NIGP01000273, NIGP01001962, NIGP01001190, NIGP01000035, NIGP01000606, NIGP01000758, NIGP01000141, NIGP01002279, NIGP01001766, NIGP01000883, NIGP01002290, NIGP01001662, NIGP01000186, NIGP01000499, NIGP01001644, NIGP01000073, NIGP01001882, NIGP01000994, NIGP01002119, NIGP01001183, NIGP01001903, NIGP01001431, NIGP01000483, NIGP01000567, NIGP01001881, NIGP01000702, NIGP01002190, NIGP01001092, NIGP01000479, NIGP01001537, NIGP01000368, NIGP01000370, NIGP01001718, NIGP01000776, NIGP01002051, NIGP01000277, NIGP01001963, NIGP01001236, NIGP01000235, NIGP01001541, NIGP01001243, NIGP01001310, NIGP01001099, NIGP01001397, NIGP01001362, NIGP01001221, NIGP01001242, NIGP01001125, NIGP01002299, NIGP01001378, NIGP01001167, NIGP01001613, NIGP01000255, NIGP01001848, NIGP01001598, NIGP01000032, NIGP01002133, NIGP01001985, NIGP01002124, NIGP01000310, NIGP01001913, NIGP01001263, NIGP01001612, NIGP01002129, NIGP01000617, NIGP01000696, NIGP01000474, NIGP01001972, NIGP01001514, NIGP01001294, NIGP01002029, NIGP01000327, NIGP01001919, NIGP01000809, NIGP01001327, NIGP01000548, NIGP01000920, NIGP01000916, NIGP01000760, NIGP01002044, NIGP01000123, NIGP01000728, NIGP01002121, NIGP01001977, NIGP01001060, NIGP01001584, NIGP01001622, NIGP01000148, NIGP01000031, NIGP01002054, NIGP01001392, NIGP01001540, NIGP01002191, NIGP01000486, NIGP01000424, NIGP01001542, NIGP01000580, NIGP01000381, NIGP01000620, NIGP01000046, NIGP01000403, NIGP01001704, NIGP01000568, NIGP01000289, NIGP01001415, NIGP01002154, NIGP01000975, NIGP01001072, NIGP01000583, NIGP01000167, NIGP01002163, NIGP01001870, NIGP01001035, NIGP01000103, NIGP01000014, NIGP01002169, NIGP01001833, NIGP01002283, NIGP01000596, NIGP01001807, NIGP01000375, NIGP01000852, NIGP01000344, NIGP01000757, NIGP01001805, NIGP01001700, NIGP01000713, NIGP01001890, NIGP01001994, NIGP01000805, NIGP01002180, NIGP01000621, NIGP01001989, NIGP01001813, NIGP01000786, NIGP01002189, NIGP01001530, NIGP01000107, NIGP01002228, NIGP01000329, NIGP01002110, NIGP01002128, NIGP01000999, NIGP01001595, NIGP01002288, NIGP01002186, NIGP01000330, NIGP01001240, NIGP01001991, NIGP01001153, NIGP01000654, NIGP01000652, NIGP01000882, NIGP01001067, NIGP01000238, NIGP01000742, NIGP01001178, NIGP01002298, NIGP01001743, NIGP01000261, NIGP01001901, NIGP01002296, NIGP01000546, NIGP01000421, NIGP01000960, NIGP01001079, NIGP01000306, NIGP01001626, NIGP01000191, NIGP01000364, NIGP01000419, NIGP01000585, NIGP01002015, NIGP01001589, NIGP01000655, NIGP01001674, NIGP01001692, NIGP01000862, NIGP01002049, NIGP01001889, NIGP01001726, NIGP01002066, NIGP01001932, NIGP01000267, NIGP01002050, NIGP01000719, NIGP01001083, NIGP01000171, NIGP01001491, NIGP01000202, NIGP01001089, NIGP01000954, NIGP01001830, NIGP01000660, NIGP01000801, NIGP01001765, NIGP01000586, NIGP01000795, NIGP01000642, NIGP01000937, NIGP01000884, NIGP01001532, NIGP01000442, NIGP01001515, NIGP01000346, NIGP01000147, NIGP01000873, NIGP01000114, NIGP01000324, NIGP01002306, NIGP01000048, NIGP01001452, NIGP01000412, NIGP01000984, NIGP01000145, NIGP01001501, NIGP01001715, NIGP01002116, NIGP01000756, NIGP01000889, NIGP01001482, NIGP01000989, NIGP01000717, NIGP01001619, NIGP01001043, NIGP01001899, NIGP01000155, NIGP01001762, NIGP01000781, NIGP01002305, NIGP01000164, NIGP01000833, NIGP01001091, NIGP01000065, NIGP01000420, NIGP01002079, NIGP01002292, NIGP01000974, NIGP01001152, NIGP01000120, NIGP01000331, NIGP01000927, NIGP01000691, NIGP01001262, NIGP01002092, NIGP01000940, NIGP01000079, NIGP01000509, NIGP01001110, NIGP01000926, NIGP01001800, NIGP01000814, NIGP01001596, NIGP01002000, NIGP01002304, NIGP01000200, NIGP01000615, NIGP01002003, NIGP01000224, NIGP01001174, NIGP01001823, NIGP01002053, NIGP01001824, NIGP01001173, NIGP01001872, NIGP01000491, NIGP01000284, NIGP01000601, NIGP01000498, NIGP01001130, NIGP01000314, NIGP01001529, NIGP01001594, NIGP01000704, NIGP01001590, NIGP01001832, NIG

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': NIGP01000072, NIGP01000780, NIGP01001781, NIGP01000364, NIGP01001501, NIGP01001668, NIGP01000232, NIGP01000089, NIGP01001701, NIGP01000966, NIGP01002125, NIGP01001113, NIGP01002309, NIGP01001886, NIGP01000294, NIGP01000802, NIGP01001704, NIGP01000156, NIGP01002129, NIGP01001240, NIGP01000377, NIGP01000546, NIGP01000721, NIGP01000576, NIGP01001822, NIGP01000642, NIGP01001745, NIGP01000324, NIGP01000342, NIGP01001152, NIGP01001799, NIGP01000224, NIGP01000729, NIGP01000891, NIGP01001141, NIGP01000949, NIGP01001337, NIGP01001165, NIGP01001171, NIGP01001434, NIGP01001277, NIGP01001657, NIGP01002239, NIGP01002034, NIGP01000033, NIGP01000602, NIGP01000197, NIGP01000817, NIGP01001870, NIGP01000103, NIGP01001079, NIGP01000222, NIGP01001605, NIGP01002112, NIGP01000830, NIGP01001931, NIGP01000693, NIGP01000085, NIGP01002198, NIGP01001442, NIGP01001291, NIGP01001378, NIGP01000019, NIGP01002192, NIGP01000304, NIGP01000292, NIGP01000034, NIGP01002253, NIGP01002196, NIGP01001919, NIGP01000497, NIGP01000791, NIGP01001612, NIGP01000728, NIGP01000213, NIGP01000486, NIGP01000583, NIGP01002202, NIGP01001890, NIGP01001713, NIGP01000882, NIGP01000310, NIGP01000872, NIGP01002015, NIGP01002007, NIGP01000862, NIGP01002066, NIGP01001684, NIGP01000841, NIGP01001981, NIGP01000260, NIGP01000155, NIGP01001485, NIGP01000910, NIGP01000927, NIGP01000738, NIGP01000474, NIGP01002000, NIGP01001183, NIGP01000109, NIGP01000733, NIGP01000626, NIGP01000625, NIGP01001071, NIGP01000488, NIGP01001718, NIGP01001840, NIGP01002036, NIGP01000798, NIGP01000485, NIGP01000812, NIGP01001377, NIGP01001243, NIGP01002032, NIGP01001344, NIGP01001131, NIGP01000541, NIGP01000578, NIGP01001934, NIGP01000747, NIGP01001925, NIGP01000381, NIGP01001017, NIGP01002031, NIGP01001114, NIGP01002065, NIGP01000852, NIGP01000246, NIGP01000049, NIGP01002229, NIGP01000674, NIGP01000421, NIGP01001996, NIGP01001400, NIGP01000834, NIGP01002049, NIGP01001090, NIGP01001585, NIGP01000937, NIGP01001555, NIGP01001656, NIGP01000756, NIGP01000420, NIGP01001766, NIGP01001800, NIGP01001685, NIGP01001418, NIGP01001529, NIGP01001955, NIGP01002010, NIGP01000771, NIGP01000462, NIGP01001788, NIGP01000131, NIGP01001199, NIGP01002085, NIGP01002150, NIGP01001245, NIGP01001107, NIGP01002203, NIGP01002127, NIGP01001514, NIGP01001294, NIGP01001039, NIGP01002289, NIGP01000809, NIGP01001327, NIGP01000398, NIGP01000361, NIGP01001757, NIGP01000039, NIGP01001024, NIGP01000142, NIGP01000577, NIGP01000009, NIGP01000450, NIGP01001516, NIGP01001961, NIGP01001764, NIGP01001058, NIGP01000464, NIGP01001540, NIGP01002191, NIGP01000424, NIGP01000580, NIGP01000896, NIGP01001053, NIGP01000568, NIGP01002126, NIGP01001415, NIGP01001499, NIGP01000523, NIGP01001035, NIGP01000367, NIGP01000823, NIGP01001819, NIGP01000969, NIGP01001059, NIGP01000348, NIGP01000447, NIGP01000047, NIGP01001958, NIGP01001994, NIGP01000805, NIGP01001989, NIGP01000209, NIGP01001813, NIGP01002084, NIGP01000005, NIGP01002189, NIGP01000919, NIGP01000644, NIGP01000557, NIGP01001952, NIGP01002193, NIGP01002177, NIGP01001230, NIGP01001991, NIGP01001046, NIGP01000017, NIGP01000942, NIGP01000560, NIGP01001081, NIGP01000652, NIGP01001783, NIGP01000055, NIGP01000238, NIGP01001015, NIGP01001901, NIGP01000960, NIGP01000093, NIGP01001778, NIGP01000589, NIGP01001406, NIGP01000353, NIGP01001512, NIGP01001626, NIGP01002217, NIGP01000585, NIGP01002097, NIGP01001575, NIGP01000708, NIGP01000783, NIGP01000143, NIGP01000696, NIGP01001083, NIGP01002258, NIGP01001502, NIGP01001547, NIGP01000412, NIGP01000145, NIGP01001983, NIGP01000889, NIGP01000606, NIGP01000717, NIGP01001619, NIGP01000758, NIGP01002294, NIGP01000781, NIGP01002305, NIGP01000833, NIGP01000065, NIGP01000151, NIGP01002079, NIGP01000883, NIGP01002290, NIGP01000120, NIGP01001731, NIGP01002008, NIGP01002023, NIGP01001689, NIGP01002038, NIGP01001644, NIGP01001382, NIGP01002003, NIGP01000296, NIGP01001824, NIGP01002262, NIGP01001173, NIGP01001706, NIGP01000284, NIGP01000822, NIGP01001916, NIGP01000339, NIGP01001130, NIGP01001594, NIGP01000690, NIGP01000653, NIGP01000111, NIGP01001296, NIGP01002281, NIGP01000922, NIGP01001974, NIGP01001287, NIGP01000506, NIGP01000551, NIGP01000905, NIGP01000071, NIGP01000270, NIGP01002080, NIGP01002190, NIGP01000686, NIGP01001044, NIGP01000773, NIGP01001537, NIGP01001607, NIGP01000762, NIGP01001040, NIGP01000365, NIGP01002051, NIGP01000248, NIGP01001912, NIGP01000816, NIGP01002108, NIGP01001299, NIGP01000952, NIGP01002060, NIGP01001861, NIGP01001177, NIGP01002124, NIGP01001732, NIGP01001236, NIGP01002274, NIGP01001609, NIGP01000860, NIGP01002259, NIGP01001550, NIGP01000231, NIGP01001417, NIGP01000868, NIGP01001364, NIGP01000337, NIGP01001433, NIGP01001239, NIGP01001397, NIGP01001449, NIGP01001360, NIGP01001318, NIGP01001483, NIGP01001117, NIGP01001539, NIGP01002211, NIGP01001125, NIGP01002220, NIGP01001365, NIGP01001300, NIGP01001468, NIGP01001453, NIGP01001353, NIGP01001157, NIGP01001188, NIGP01001486, NIGP01001372, NIGP01000503, NIGP01001135, NIGP01001126, NIGP01001387, NIGP01001166, NIGP01001307, NIGP01002254, NIGP01001127, NIGP01001720, NIGP01001219, NIGP01002245, NIGP01002256, NIGP01002226, NIGP01000875, NIGP01002266, NIGP01000425, NIGP01000242, NIGP01002029, NIGP01002269, NIGP01001661, NIGP01000697, NIGP01001062, NIGP01000327, NIGP01001988, NIGP01000650, NIGP01000504, NIGP01002024, NIGP01001469, NIGP01000920, NIGP01000417, NIGP01000384, NIGP01000646, NIGP01000916, NIGP01000760, NIGP01002133, NIGP01000123, NIGP01001956, NIGP01001736, NIGP01000290, NIGP01002103, NIGP01002121, NIGP01001060, NIGP01000148, NIGP01000463, NIGP01000736, NIGP01001392, NIGP01000522, NIGP01001950, NIGP01000467, NIGP01000620, NIGP01000263, NIGP01000194, NIGP01000369, NIGP01002154, NIGP01000975, NIGP01001072, NIGP01002163, NIGP01000709, NIGP01000014, NIGP01001807, NIGP01000757, NIGP01001700, NIGP01000713, NIGP01000069, NIGP01000734, NIGP01002039, NIGP01000084, NIGP01001014, NIGP01002308, NIGP01000053, NIGP01002288, NIGP01000617, NIGP01000633, NIGP01000654, NIGP01001067, NIGP01000436, NIGP01000632, NIGP01000752, NIGP01000306, NIGP01000527, NIGP01000220, NIGP01000679, NIGP01000191, NIGP01002164, NIGP01001636, NIGP01000264, NIGP01001674, NIGP01000343, NIGP01001978, NIGP01000555, NIGP01001623, NIGP01000267, NIGP01000719, NIGP01000171, NIGP01000698, NIGP01000954, NIGP01001830, NIGP01000659, NIGP01000998, NIGP01000442, NIGP01002247, NIGP01000346, NIGP01000873, NIGP01000114, NIGP01002306, NIGP01000048, NIGP01001452, NIGP01000466, NIGP01001190, NIGP01000035, NIGP01001883, NIGP01001762, NIGP01000545, NIGP01000995, NIGP01000499, NIGP01000940, NIGP01001010, NIGP01000073, NIGP01001075, NIGP01001820, NIGP01002136, NIGP01000153, NIGP01001972, NIGP01001179, NIGP01000498, NIGP01000925, NIGP01000314, NIGP01001590, NIGP01001832, NIGP01002070, NIGP01001789, NIGP01000517, NIGP01000594, NIGP01001184, NIGP01001006, NIGP01000685, NIGP01000687, NIGP01001559, NIGP01001632, NIGP01000040, NIGP01001373, NIGP01001055, NIGP01001054, NIGP01002156, NIGP01001812, NIGP01001860, NIGP01001881, NIGP01000396, NIGP01000844, NIGP01001496, NIGP01001001, NIGP01001687, NIGP01000538, NIGP01000320, NIGP01001926, NIGP01001038, NIGP01000193, NIGP01001663, NIGP01000746, NIGP01001784, NIGP01002214, NIGP01001910, NIGP01000707, NIGP01000701, NIGP01000895, NIGP01000540, NIGP01001070, NIGP01001201, NIGP01001238, NIGP01000054, NIGP01000395, NIGP01001907, NIGP01001922, NIGP01001356, NIGP01000668, NIGP01001227, NIGP01000090, NIGP01000459, NIGP01000259, NIGP01000321, NIGP01000890, NIGP01001357, NIGP01001855, NIGP01002238, NIGP01000275, NIGP01000784, NIGP01000091, NIGP01001172, NIGP01000196, NIGP01001319, NIGP01001419, NIGP01001603, NIGP01001320, NIGP01001218, NIGP01000062, NIGP01001187, NIGP01001140, NIGP01002210, NIGP01001325, NIGP01001340, NIGP01001221, NIGP01001009, NIGP01000444, NIGP01001234, NIGP01001391, NIGP01001425, NIGP01002299, NIGP01001314, NIGP01001494, NIGP01001189, NIGP01000050, NIGP01001175, NIGP01000302, NIGP01000678, NIGP01000867, NIGP01000753, NIGP01001027, NIGP01001602
##   - in 'y': NIGP01000004, NIGP01000008, NIGP01000025, NIGP01000030, NIGP01000036, NIGP01000041, NIGP01000042, NIGP01

lreads_over_overpeaksdf <- lapply(lreads_over_overpeaks, as.data.frame)
lreads_over_overpeaksdf<- lapply(lreads_over_overpeaksdf, function(x) cbind(x, overlapID = paste0(x$overlapping_rf.seqnames, ":", x$overlapping_rf.start,"_", x$overlapping_rf.end)))

lreads_over_overpeaksdf<- rbindlist(lreads_over_overpeaksdf, idcol = TRUE)
lreads_over_overpeaksdf$duplicated <- paste0(lreads_over_overpeaksdf$x.name, "_", lreads_over_overpeaksdf$overlapID, "_", lreads_over_overpeaksdf$.id)
lreads_over_overpeaksdf$duplicatedoverlap <- duplicated(lreads_over_overpeaksdf$duplicated)
length(which(lreads_over_overpeaksdf$duplicatedoverlap==TRUE)) #check for duplicates; good, 0

## [1] 0

#group by sample and count pos and neg 
lreads_over_overpeaksdf <- setNames(lreads_over_overpeaksdf, gsub(".id", "sample", colnames(lreads_over_overpeaksdf )))

lread_overlap_bypeak <- lreads_over_overpeaksdf %>% group_by(.dots=c("sample","x.strand", "overlapID")) %>% summarize(count = n(),total_length = sum(x.sampleth))

#if are overlapping reads, calculate count and length bias ratios
lread <- lread_overlap_bypeak %>% group_by(.dots=c("sample","overlapID")) %>% filter(n()==2) %>% group_by(.dots=c("sample","overlapID")) %>% mutate(pos_over_neg_count = ((subset(count, x.strand=="+"))/(subset(count, x.strand=="-"))), pos_over_neg_legnth = ((subset(total_length, x.strand=="+"))/(subset(total_length, x.strand=="-"))))

lread_coll <- distinct(lread, overlapID, .keep_all = TRUE) #remove duplicate entries because have one positive and one negative read entry for each peak with the same count and length ratios

#now peaks with reads on only one strand
lread_unpair <- lread_overlap_bypeak %>% group_by(.dots=c("sample","overlapID")) %>% filter(n()==1) %>% group_by(.dots=c("sample","overlapID"))   
lread_unpair$pos_over_neg_count  <- ifelse(lread_unpair$x.strand=="+", as.numeric(paste0(lread_unpair$count)), as.numeric(1/lread_unpair$count))
lread_unpair$pos_over_neg_legnth  <- ifelse(lread_unpair$x.strand=="+", as.numeric(paste0(lread_unpair$total_length)), as.numeric(1/lread_unpair$total_length))


lread_bind <- rbind(lread_unpair, lread_coll)
lread_bind  <- as.data.frame(lread_bind)

#write.table(lread_bind, "/Users/kathryn/Reprocess_all_paper_datasets/Rmds_to_upload/To_upload/overlapping_read_counts.txt", col.names = TRUE,row.names = FALSE, quote  = FALSE, sep  = "\t")

Output file “overlapping_read_counts.txt” used to make the figure is available on my Github

Get absolute values for strand bias ratio

#User can start here with data table provided in my github
lread_bind <-read.delim("/Users/kathryn/Reprocess_all_paper_datasets/Rmds_to_upload/overlapping_read_counts.txt",  header = TRUE, stringsAsFactors = FALSE, sep= "\t")

lread_noIgG <- lread_bind[!grepl("IgG", lread_bind$sample),]

lread_noIgG$log10count <- log10(lread_noIgG$pos_over_neg_count)
lread_noIgG$log10count_nosense <- ifelse(lread_noIgG$log10count < 0, lread_noIgG$log10count * -1, lread_noIgG$log10count * 1)
lread_noIgG$log10length <- log10(lread_noIgG$pos_over_neg_legnth)
lread_noIgG$log10length_nosense <- ifelse(lread_noIgG$log10length < 0, lread_noIgG$log10length * -1, lread_noIgG$log10length * 1)

lread_Aag2 <- lread_noIgG[grepl("Aag2", lread_noIgG$sample),]
lread_aegypti <- lread_noIgG[grepl("aegypti", lread_noIgG$sample),]

Figures S5C and S5D

vert <- c(0,2)

ggplot(lread_Aag2, aes(log10count_nosense, colour = sample)) + stat_ecdf() + scale_colour_manual(values=c("#1B0B80", "#8A0F09")) + theme_bw() + geom_vline(xintercept =vert, linetype="dashed") + xlim(0, 4)

ggplot(lread_aegypti, aes(log10count_nosense, colour = sample)) + stat_ecdf() + scale_colour_manual(values=c("#3360A9", "#FA0F0C")) + theme_bw() + geom_vline(xintercept =vert, linetype="dashed") + xlim(0, 5)

wilcox.test(subset(lread_Aag2$log10count_nosense, lread_Aag2$sample=="cat_Aag2Ago1.bed"), subset(lread_Aag2$log10count_nosense, lread_Aag2$sample=="cat_Aag2Ago2.bed"),alternative = c("g"))

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  subset(lread_Aag2$log10count_nosense, lread_Aag2$sample == "cat_Aag2Ago1.bed") and subset(lread_Aag2$log10count_nosense, lread_Aag2$sample == "cat_Aag2Ago2.bed")
## W = 75844, p-value < 2.2e-16
## alternative hypothesis: true location shift is greater than 0

wilcox.test(subset(lread_aegypti$log10count_nosense, lread_aegypti$sample=="cat_aegyptiAgo1.bed"), subset(lread_aegypti$log10count_nosense, lread_aegypti$sample=="cat_aegyptiAgo2.bed"),alternative = c("g"))

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  subset(lread_aegypti$log10count_nosense, lread_aegypti$sample ==  and subset(lread_aegypti$log10count_nosense, lread_aegypti$sample ==     "cat_aegyptiAgo1.bed") and     "cat_aegyptiAgo2.bed")
## W = 52109, p-value < 2.2e-16
## alternative hypothesis: true location shift is greater than 0

overlaps_strand_bias_to_upload

KRG

6/28/2020

Get strand bias ratio for overlapping peaks

Get absolute values for strand bias ratio

Figures S5C and S5D