BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004091.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,227,196 number of mapped reads = 1,830,524 (82.19%) number of supplementary alignments = 26,654 (1.2%) number of secondary alignments = 0 number of mapped bases = 118,172,190 bp number of sequenced bases = 118,109,831 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 214,287 duplication rate = 9.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5279 >>>>>>> ACTG content number of A's = 32,482,907 bp (27.5%) number of C's = 21,372,474 bp (18.1%) number of T's = 37,853,025 bp (32.05%) number of G's = 26,355,645 bp (22.31%) number of N's = 45,780 bp (0.04%) GC percentage = 40.41% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 990,686 number of insertions = 8,183 mapped reads with insertion percentage = 0.44% number of deletions = 37,592 mapped reads with deletion percentage = 2.03% homopolymer indels = 44.91% >>>>>>> Coverage mean coverageData = 0.0382X std coverageData = 0.3892X There is a 2.28% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9905705 0.03974194712237046 0.6936848899229571 chr2 243199373 2652569 0.01090697302085561 0.3454064369487407 chr3 198022430 5614546 0.02835308101208535 0.25551068288516343 chr4 191154276 6290501 0.032907979521211446 0.2795714503345169 chr5 180915260 7475471 0.041320289952323536 0.3155400147183089 chr6 171115067 3633415 0.021233752606951907 0.2352203670156724 chr7 159138663 12385712 0.07782968492075366 0.5098821375843772 chr8 146364022 5113252 0.034935170065222725 0.5045607359843509 chr9 141213431 1705195 0.01207530323372711 0.21369342292817178 chr10 135534747 5082854 0.03750222074048657 0.394496387012172 chr11 135006516 3266961 0.024198543128096127 0.2525183989629229 chr12 133851895 9940243 0.07426299792020127 0.4208060854187746 chr13 115169878 4162422 0.036141585562850034 0.29256993891612737 chr14 107349540 3715830 0.03461430761603636 0.2884214650655436 chr15 102531392 8491909 0.08282252717294622 0.44818676736987384 chr16 90354753 6450171 0.0713871798199703 0.4187691318665518 chr17 81195210 680103 0.008376146819498342 0.1299439164339376 chr18 78077248 813108 0.010414147793733713 0.34625505376014987 chr19 59128983 4337625 0.07335869450012357 0.5576557318053522 chr20 63025520 7445841 0.11814009626576663 0.5417228406932433 chr21 48129895 395687 0.008221231315796555 0.13251536389000806 chr22 51304566 1173930 0.022881589135750606 0.22398047596510567 chrMT 16571 33950 2.048759881721079 2.5399859950129082 chrX 155270560 7118822 0.04584785422297698 0.3310180271440184 chrY 59373566 286368 0.004823156486844667 0.1258114737705903