BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716276.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 = 1,517,148 number of mapped reads = 1,352,743 (89.16%) number of supplementary alignments = 5,659 (0.37%) number of secondary alignments = 0 number of mapped bases = 78,650,525 bp number of sequenced bases = 78,628,977 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,144 duplication rate = 3.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4948 >>>>>>> ACTG content number of A's = 20,311,935 bp (25.83%) number of C's = 14,723,703 bp (18.73%) number of T's = 25,230,320 bp (32.09%) number of G's = 18,360,726 bp (23.35%) number of N's = 2,293 bp (0%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 384,168 number of insertions = 5,256 mapped reads with insertion percentage = 0.39% number of deletions = 13,489 mapped reads with deletion percentage = 0.99% homopolymer indels = 42.29% >>>>>>> Coverage mean coverageData = 0.0254X std coverageData = 0.2351X There is a 2.27% of reference with a coverageData >= 1X There is a 0.2% 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% 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 6215388 0.02493629895509869 0.40324619556519004 chr2 243199373 6880415 0.028291253037070946 0.329188875411102 chr3 198022430 5169422 0.026105234644378417 0.17727479984977726 chr4 191154276 5128292 0.026828026593556296 0.1882718351043164 chr5 180915260 5040152 0.027859186671152007 0.18329636509564448 chr6 171115067 4555357 0.026621600773472507 0.20581490335729843 chr7 159138663 4462960 0.02804447339110798 0.2537000561022919 chr8 146364022 3933938 0.026877766450009142 0.22456429802004202 chr9 141213431 3304985 0.02340418313326018 0.1944176151421454 chr10 135534747 3856923 0.028457078980639556 0.2370795705310201 chr11 135006516 3685038 0.027295260326546018 0.21688319718207016 chr12 133851895 3421102 0.02555886115769971 0.17731670953045392 chr13 115169878 2426771 0.021071230100634473 0.15946423525152956 chr14 107349540 2442859 0.02275611986786343 0.16970596860978462 chr15 102531392 2381456 0.023226603614237482 0.16736606297128281 chr16 90354753 2215348 0.024518333861197096 0.17929234633221303 chr17 81195210 2011282 0.024770944000267997 0.17943532144159266 chr18 78077248 2007525 0.025712035854542414 0.2868753320919622 chr19 59128983 1603124 0.027112321549653578 0.29028771300559447 chr20 63025520 1621913 0.0257342263895641 0.17750127199235374 chr21 48129895 763799 0.015869533893643442 0.15131194926115157 chr22 51304566 878454 0.01712233566111835 0.14426354453816578 chrMT 16571 13201 0.7966326715346087 1.0071208250005388 chrX 155270560 4404303 0.028365344982332775 0.19897183657864978 chrY 59373566 226518 0.0038151321414651093 0.10281476245092841