BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716651.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 = 2,645,800 number of mapped reads = 2,434,437 (92.01%) number of supplementary alignments = 72,192 (2.73%) number of secondary alignments = 0 number of mapped bases = 181,679,756 bp number of sequenced bases = 181,613,939 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,070 duplication rate = 2.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8352 >>>>>>> ACTG content number of A's = 46,446,570 bp (25.57%) number of C's = 37,843,712 bp (20.84%) number of T's = 53,835,987 bp (29.64%) number of G's = 43,466,002 bp (23.93%) number of N's = 21,668 bp (0.01%) GC percentage = 44.77% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,363,596 number of insertions = 15,433 mapped reads with insertion percentage = 0.62% number of deletions = 37,561 mapped reads with deletion percentage = 1.52% homopolymer indels = 38.87% >>>>>>> Coverage mean coverageData = 0.0587X std coverageData = 0.4462X There is a 4.97% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 17351066 0.06961292987109549 0.710189542569761 chr2 243199373 15213294 0.06255482410310326 0.708087999584736 chr3 198022430 14394567 0.07269159862344887 0.3148276823758111 chr4 191154276 7030253 0.03677790079882911 0.24478811410107373 chr5 180915260 11393181 0.06297523492490352 0.28594104959216626 chr6 171115067 12233243 0.07149132577553793 0.35372893354450863 chr7 159138663 9448287 0.05937141120759573 0.5919354350390578 chr8 146364022 11409995 0.07795628217978323 0.5757881400813284 chr9 141213431 8157370 0.05776624746126308 0.3964108762637391 chr10 135534747 9896390 0.07301736432208045 0.5059429226837384 chr11 135006516 7005789 0.0518922286684296 0.3689450912469823 chr12 133851895 7565001 0.05651769816183776 0.27448720579215163 chr13 115169878 6273618 0.054472732878991154 0.26836534654854655 chr14 107349540 4366454 0.040675106758724815 0.24955034322490688 chr15 102531392 3846578 0.0375161004348795 0.22267011268996212 chr16 90354753 4998951 0.05532582220660821 0.29897634413291824 chr17 81195210 6445174 0.07937874660340186 0.37089524816149433 chr18 78077248 4733891 0.06063086393618791 0.5128470366850107 chr19 59128983 3794728 0.0641771227487542 0.623782958161632 chr20 63025520 3252679 0.051608919688405586 0.2660095822035252 chr21 48129895 2352329 0.048874592392108895 0.27179569364928025 chr22 51304566 2660783 0.0518624989440511 0.26772814405302414 chrMT 16571 18411 1.1110373544143384 1.8635455405922305 chrX 155270560 7400098 0.047659375995037306 0.29024259477335845 chrY 59373566 437626 0.007370721172449033 0.24391879052264043