BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716874.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 = 795,510 number of mapped reads = 728,188 (91.54%) number of supplementary alignments = 1,317 (0.17%) number of secondary alignments = 0 number of mapped bases = 42,036,331 bp number of sequenced bases = 42,023,115 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,837 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3402 >>>>>>> ACTG content number of A's = 10,954,656 bp (26.07%) number of C's = 7,742,744 bp (18.42%) number of T's = 12,975,091 bp (30.88%) number of G's = 10,350,262 bp (24.63%) number of N's = 362 bp (0%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 204,276 number of insertions = 3,173 mapped reads with insertion percentage = 0.43% number of deletions = 8,391 mapped reads with deletion percentage = 1.14% homopolymer indels = 41.17% >>>>>>> Coverage mean coverageData = 0.0136X std coverageData = 0.1491X There is a 1.27% of reference with a coverageData >= 1X There is a 0.06% 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 4822023 0.019346082190904553 0.19363175840496413 chr2 243199373 4299057 0.017677089159271804 0.19531455088845182 chr3 198022430 2781341 0.014045585644010126 0.12514473064427722 chr4 191154276 1778403 0.009303495779503254 0.10662366361811362 chr5 180915260 2940335 0.016252553819948633 0.13391979240927532 chr6 171115067 1533855 0.008963880427899432 0.10920979756087953 chr7 159138663 2792688 0.017548771287590872 0.23292020943566952 chr8 146364022 1908709 0.013040834584335213 0.13157485990243856 chr9 141213431 1313527 0.009301714367381952 0.12276076118288927 chr10 135534747 1991296 0.01469214385297078 0.17603822919340248 chr11 135006516 1852109 0.013718663771754543 0.1444116203755019 chr12 133851895 1696941 0.012677751032213627 0.11831927791891701 chr13 115169878 1162450 0.010093350971510102 0.10556123042972493 chr14 107349540 879054 0.008188707655384457 0.09803419854417993 chr15 102531392 1826531 0.01781435874780672 0.14108532042914493 chr16 90354753 1238530 0.013707413930952808 0.13064263646569926 chr17 81195210 1497759 0.018446396037401714 0.14739291244048996 chr18 78077248 1392193 0.01783096914481412 0.22410688908859605 chr19 59128983 627440 0.010611378179800589 0.14849218397867572 chr20 63025520 1076109 0.017074178840571247 0.1373765295414165 chr21 48129895 522753 0.010861295251111602 0.11180409286396026 chr22 51304566 461822 0.00900157697464978 0.09920159564320125 chrMT 16571 1864 0.11248566773278619 0.36022833157422784 chrX 155270560 1539379 0.009914171752842265 0.11474982705183853 chrY 59373566 100163 0.0016869965331036375 0.05746869680808233