BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525107.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 = 680,761 number of mapped reads = 588,404 (86.43%) number of supplementary alignments = 14,527 (2.13%) number of secondary alignments = 0 number of mapped bases = 44,976,488 bp number of sequenced bases = 44,959,103 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,038 duplication rate = 1.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5101 >>>>>>> ACTG content number of A's = 12,172,013 bp (27.07%) number of C's = 8,569,997 bp (19.06%) number of T's = 14,055,902 bp (31.26%) number of G's = 10,159,681 bp (22.6%) number of N's = 1,510 bp (0%) GC percentage = 41.66% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 329,725 number of insertions = 4,098 mapped reads with insertion percentage = 0.69% number of deletions = 10,221 mapped reads with deletion percentage = 1.72% homopolymer indels = 40.73% >>>>>>> Coverage mean coverageData = 0.0145X std coverageData = 0.1748X There is a 1.36% 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 3517593 0.014112674969022444 0.23455085679668716 chr2 243199373 3922039 0.016126846675710797 0.2428636013671142 chr3 198022430 3019042 0.015245959763245002 0.12834572094112986 chr4 191154276 2975185 0.015564313089182477 0.13361719329056512 chr5 180915260 2804032 0.015499145843197528 0.1313984751640468 chr6 171115067 2650995 0.015492469754285285 0.14051112636460833 chr7 159138663 2512721 0.0157895067900627 0.2393111521474804 chr8 146364022 2372897 0.01621229703567452 0.22906782764037892 chr9 141213431 1889508 0.013380511942946843 0.17435869250485728 chr10 135534747 2055895 0.015168767017361239 0.1659287909066512 chr11 135006516 2041771 0.015123499668712287 0.17761355181714164 chr12 133851895 2027131 0.01514458200236911 0.12864734220077811 chr13 115169878 1467180 0.012739268509080127 0.11686589126744344 chr14 107349540 1350914 0.012584255135140774 0.1298925887060828 chr15 102531392 1257289 0.012262478597774231 0.11478517006838125 chr16 90354753 1211531 0.013408602865640062 0.1262756168033357 chr17 81195210 1132080 0.013942694402785583 0.1425823066227717 chr18 78077248 1280538 0.01640091105670118 0.27881219335671076 chr19 59128983 820890 0.013883039388653108 0.19024467147993826 chr20 63025520 883302 0.014014989483625047 0.12413929036615956 chr21 48129895 602818 0.012524814359142067 0.12082659200037665 chr22 51304566 451202 0.008794577854922308 0.09780664144501737 chrMT 16571 945 0.0570273369138857 0.36676789289940004 chrX 155270560 2631990 0.016950991868645286 0.15450280757233478 chrY 59373566 97000 0.0016337236675324504 0.04881022479515181