BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068057.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 = 6,324,369 number of mapped reads = 5,904,795 (93.37%) number of supplementary alignments = 60,667 (0.96%) number of secondary alignments = 0 number of mapped bases = 382,821,458 bp number of sequenced bases = 382,685,726 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,915,320 duplication rate = 18.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0234 >>>>>>> ACTG content number of A's = 96,358,409 bp (25.18%) number of C's = 72,767,887 bp (19.02%) number of T's = 120,270,367 bp (31.43%) number of G's = 93,245,060 bp (24.37%) number of N's = 44,003 bp (0.01%) GC percentage = 43.38% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,940,294 number of insertions = 24,691 mapped reads with insertion percentage = 0.41% number of deletions = 77,249 mapped reads with deletion percentage = 1.3% homopolymer indels = 44.51% >>>>>>> Coverage mean coverageData = 0.1237X std coverageData = 1.2934X There is a 4.09% of reference with a coverageData >= 1X There is a 2.44% of reference with a coverageData >= 2X There is a 1.66% of reference with a coverageData >= 3X There is a 1.15% of reference with a coverageData >= 4X There is a 0.81% of reference with a coverageData >= 5X There is a 0.57% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 47810834 0.191818314466707 1.8516319687158016 chr2 243199373 24397667 0.10031961307729194 2.3455439375230664 chr3 198022430 24512675 0.12378736590597338 0.821269647967943 chr4 191154276 24579782 0.12858609555770545 0.8772858721029242 chr5 180915260 18012466 0.09956299982654863 0.7285390282873891 chr6 171115067 20096886 0.11744661853768844 1.0291239889778314 chr7 159138663 33680228 0.21164076262221707 2.219730373422623 chr8 146364022 12698736 0.08676132171333745 1.3759737054711296 chr9 141213431 14917371 0.10563705516085081 0.8776035094835226 chr10 135534747 12971843 0.09570861559213299 0.8027009527015483 chr11 135006516 18323381 0.13572219729009227 1.0826691416189427 chr12 133851895 7623442 0.05695430759497279 0.5773521841025894 chr13 115169878 7369354 0.06398681780317593 0.6501564143142039 chr14 107349540 15043418 0.14013490882215238 0.9145699314376732 chr15 102531392 11823425 0.1153151709868525 0.8269299677411699 chr16 90354753 9918924 0.10977755647231972 0.8101057555499029 chr17 81195210 9105447 0.11214266211024025 0.8364156611056225 chr18 78077248 8590176 0.1100215007578136 1.5270329578520334 chr19 59128983 10935833 0.1849487754592363 1.3928309197857751 chr20 63025520 3394584 0.0538604679501256 0.5902713053826587 chr21 48129895 10815891 0.22472292948073125 1.1800276545422943 chr22 51304566 5363645 0.10454517829855534 0.7600733143621978 chrMT 16571 204857 12.362380061553315 11.349734967033061 chrX 155270560 29784255 0.19182164989937564 1.153432185630716 chrY 59373566 846338 0.014254457951877103 0.42322505058379317