BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716964.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 = 933,986 number of mapped reads = 872,389 (93.4%) number of supplementary alignments = 20,282 (2.17%) number of secondary alignments = 0 number of mapped bases = 68,647,374 bp number of sequenced bases = 68,619,337 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,918 duplication rate = 2.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1115 >>>>>>> ACTG content number of A's = 17,449,919 bp (25.43%) number of C's = 13,675,824 bp (19.93%) number of T's = 20,208,578 bp (29.45%) number of G's = 17,282,440 bp (25.19%) number of N's = 2,576 bp (0%) GC percentage = 45.12% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 441,884 number of insertions = 6,561 mapped reads with insertion percentage = 0.74% number of deletions = 13,233 mapped reads with deletion percentage = 1.49% homopolymer indels = 38.2% >>>>>>> Coverage mean coverageData = 0.0222X std coverageData = 0.2056X There is a 1.99% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 5658829 0.022703369713971546 0.28657613845590507 chr2 243199373 5806589 0.023875838693054527 0.22143987194169537 chr3 198022430 4419811 0.02231974933344672 0.16097112489465365 chr4 191154276 4256045 0.02226497407779672 0.22446820223782954 chr5 180915260 4052689 0.02240103460592545 0.1618889920932126 chr6 171115067 3860443 0.022560508946883093 0.16690387364916487 chr7 159138663 3753752 0.023587932242462036 0.24778037127932961 chr8 146364022 3463746 0.023665282988738857 0.19984122385863579 chr9 141213431 2805723 0.01986866957435515 0.18177046822462403 chr10 135534747 3404621 0.02511991260809304 0.2770213059602482 chr11 135006516 3200436 0.023705789133911137 0.2138255567350951 chr12 133851895 3032804 0.02265790857873174 0.16474778632573706 chr13 115169878 2058391 0.017872650694307414 0.14514859830899018 chr14 107349540 2031364 0.01892289431328723 0.1614860043557648 chr15 102531392 2007885 0.019583124356684828 0.15206323242046774 chr16 90354753 2167048 0.023983774268078625 0.17799740777651818 chr17 81195210 1946426 0.023972177669101417 0.18203255226429205 chr18 78077248 1820887 0.023321608364065292 0.2607443807372447 chr19 59128983 1506822 0.025483644797340756 0.22259878205714065 chr20 63025520 1571006 0.024926505961394684 0.18081642735948833 chr21 48129895 922747 0.019172013568697792 0.19042361221777768 chr22 51304566 936374 0.01825128001277703 0.14810926821288944 chrMT 16571 7599 0.45857220445356345 0.7914601737370802 chrX 155270560 3688971 0.023758341568420955 0.17383065159340974 chrY 59373566 266366 0.004486272561092255 0.209689497479815