BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013249.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 = 1,467,663 number of mapped reads = 338,814 (23.09%) number of supplementary alignments = 3,347 (0.23%) number of secondary alignments = 0 number of mapped bases = 21,391,561 bp number of sequenced bases = 21,366,368 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,644 duplication rate = 3.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3511 >>>>>>> ACTG content number of A's = 6,015,925 bp (28.16%) number of C's = 3,678,644 bp (17.22%) number of T's = 7,080,575 bp (33.14%) number of G's = 4,586,842 bp (21.47%) number of N's = 4,382 bp (0.02%) GC percentage = 38.68% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 235,010 number of insertions = 1,736 mapped reads with insertion percentage = 0.5% number of deletions = 14,256 mapped reads with deletion percentage = 4.09% homopolymer indels = 41.74% >>>>>>> Coverage mean coverageData = 0.0069X std coverageData = 0.1218X There is a 0.59% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 1396296 0.005601976012729774 0.22512642619263462 chr2 243199373 2762922 0.01136072830253555 0.16025476208151102 chr3 198022430 1516596 0.007658708157454688 0.1003049619026392 chr4 191154276 1584104 0.00828704454406241 0.10595244824540155 chr5 180915260 755956 0.004178508767032698 0.07265861833891937 chr6 171115067 836891 0.0048908083587987025 0.09174674052572185 chr7 159138663 1426257 0.008962353793307915 0.13110959796692712 chr8 146364022 2017713 0.01378558044817872 0.1641252926202061 chr9 141213431 396425 0.0028072754637623668 0.06925874598038273 chr10 135534747 1147126 0.008463704145181309 0.11934929647129933 chr11 135006516 1045163 0.007741574488152853 0.103161649259665 chr12 133851895 617932 0.004616535313153393 0.07709496388304385 chr13 115169878 369692 0.0032099712739124373 0.06620890225137865 chr14 107349540 586019 0.005458980075741359 0.0847844803405763 chr15 102531392 461818 0.004504162003379414 0.07532441530645141 chr16 90354753 867143 0.00959709335932776 0.11318848971310352 chr17 81195210 328634 0.0040474555087670816 0.07381338389142718 chr18 78077248 553007 0.007082818800170826 0.12169877841752852 chr19 59128983 389380 0.0065852646239493075 0.14368497471787434 chr20 63025520 449794 0.007136696373151701 0.09661700431076842 chr21 48129895 352556 0.007325093894345707 0.09793113310475014 chr22 51304566 107267 0.002090788566460147 0.05020654119682699 chrMT 16571 3680 0.2220747088286766 0.5286302554586993 chrX 155270560 1349601 0.008691931039599522 0.10829779624955659 chrY 59373566 69589 0.0011720535701022236 0.04748014579037871