BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716858.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 = 2,090,936 number of mapped reads = 1,971,715 (94.3%) number of supplementary alignments = 41,490 (1.98%) number of secondary alignments = 0 number of mapped bases = 152,283,912 bp number of sequenced bases = 152,224,939 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,459 duplication rate = 4.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5843 >>>>>>> ACTG content number of A's = 38,316,119 bp (25.17%) number of C's = 31,758,371 bp (20.86%) number of T's = 44,987,992 bp (29.55%) number of G's = 37,156,722 bp (24.41%) number of N's = 5,735 bp (0%) GC percentage = 45.27% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 968,887 number of insertions = 14,190 mapped reads with insertion percentage = 0.71% number of deletions = 28,219 mapped reads with deletion percentage = 1.4% homopolymer indels = 37.62% >>>>>>> Coverage mean coverageData = 0.0492X std coverageData = 0.3878X There is a 3.98% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 16923786 0.06789867135376164 0.719041222182673 chr2 243199373 14422930 0.05930496375087283 0.41931303789758206 chr3 198022430 9831867 0.04965026941644944 0.2668550977745653 chr4 191154276 7450063 0.0389740849950958 0.33974708392376174 chr5 180915260 7766034 0.042926362320127115 0.2489696338017374 chr6 171115067 9613223 0.05617987456358826 0.29961173460361523 chr7 159138663 9632065 0.06052624056543695 0.5247826183937839 chr8 146364022 9408571 0.06428199274272471 0.4132916269242622 chr9 141213431 4574267 0.03239257744541311 0.271135473495657 chr10 135534747 7866037 0.05803705082357958 0.529128130655741 chr11 135006516 4621044 0.03422830346944143 0.3035051633141952 chr12 133851895 5611600 0.0419239488540674 0.24421075735118516 chr13 115169878 2878165 0.02499060561651372 0.18477535554551294 chr14 107349540 2919777 0.027198784456831392 0.2127531860515623 chr15 102531392 3184842 0.031062116078556704 0.20771027955539528 chr16 90354753 4510662 0.049921690339854066 0.2839322024417205 chr17 81195210 3848639 0.04739982814257147 0.28559864955654646 chr18 78077248 4519586 0.05788608225535818 0.404485780053491 chr19 59128983 3774964 0.06384287042447526 0.5314123933503555 chr20 63025520 4117029 0.06532320558402374 0.32280228463815364 chr21 48129895 2344803 0.04871822388143585 0.3357746156320136 chr22 51304566 2433944 0.04744107961073094 0.27845244739468683 chrMT 16571 21666 1.3074648482288336 1.5196132133452533 chrX 155270560 9510803 0.0612530991064887 0.3123682440236863 chrY 59373566 497545 0.008379907651159103 0.2978885944834362