BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716791.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,932,139 number of mapped reads = 1,705,680 (88.28%) number of supplementary alignments = 6,469 (0.33%) number of secondary alignments = 0 number of mapped bases = 96,700,350 bp number of sequenced bases = 96,671,608 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,280 duplication rate = 1.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0813 >>>>>>> ACTG content number of A's = 24,145,928 bp (24.98%) number of C's = 19,612,563 bp (20.29%) number of T's = 29,740,946 bp (30.76%) number of G's = 23,171,507 bp (23.97%) number of N's = 664 bp (0%) GC percentage = 44.26% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 508,196 number of insertions = 5,626 mapped reads with insertion percentage = 0.33% number of deletions = 17,967 mapped reads with deletion percentage = 1.04% homopolymer indels = 41.86% >>>>>>> Coverage mean coverageData = 0.0312X std coverageData = 0.2598X There is a 2.81% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 8155267 0.03271914415812027 0.32974338095543293 chr2 243199373 7607236 0.03127983393279554 0.39734197068536065 chr3 198022430 5562835 0.028091943927766164 0.1863608536362534 chr4 191154276 5862929 0.030671189380037725 0.20684430327284903 chr5 180915260 5504611 0.030426460432359328 0.1901454166954603 chr6 171115067 5154303 0.030121853617951715 0.2302862872633325 chr7 159138663 5500230 0.03456249974903962 0.37395344603444475 chr8 146364022 4997328 0.03414314482284451 0.24796482054347552 chr9 141213431 3231153 0.022881343347574353 0.19459272557945703 chr10 135534747 4240063 0.03128395554536284 0.31387223032810724 chr11 135006516 3423814 0.025360361125088215 0.2160399056250089 chr12 133851895 4795828 0.035829361997452486 0.20689563492859936 chr13 115169878 2903613 0.025211566170105695 0.1736139941994101 chr14 107349540 3209823 0.029900668414601497 0.19436945117793283 chr15 102531392 3592849 0.035041453450666116 0.2115588103704155 chr16 90354753 3382639 0.03743731112850256 0.22567444388993926 chr17 81195210 4379211 0.05393435154610721 0.2679901125016635 chr18 78077248 1790570 0.022933313428260178 0.2985619581660792 chr19 59128983 2593891 0.04386835132949944 0.31718598525141967 chr20 63025520 3145423 0.0499071328566587 0.25812059656509156 chr21 48129895 1203011 0.02499508881122637 0.18760096661346912 chr22 51304566 912688 0.017789605704880147 0.14868339522907853 chrMT 16571 3338 0.20143624404079416 0.4777093812511522 chrX 155270560 5261657 0.03388702275563378 0.21499588673709913 chrY 59373566 286040 0.004817632142896723 0.12865328171575977