BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716344.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 = 1,103,711 number of mapped reads = 986,437 (89.37%) number of supplementary alignments = 5,878 (0.53%) number of secondary alignments = 0 number of mapped bases = 56,894,239 bp number of sequenced bases = 56,877,924 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,452 duplication rate = 2.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6587 >>>>>>> ACTG content number of A's = 14,671,734 bp (25.8%) number of C's = 10,932,921 bp (19.22%) number of T's = 17,938,390 bp (31.54%) number of G's = 13,334,145 bp (23.44%) number of N's = 734 bp (0%) GC percentage = 42.67% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 284,772 number of insertions = 3,980 mapped reads with insertion percentage = 0.4% number of deletions = 10,225 mapped reads with deletion percentage = 1.03% homopolymer indels = 39.62% >>>>>>> Coverage mean coverageData = 0.0184X std coverageData = 0.1814X There is a 1.69% of reference with a coverageData >= 1X There is a 0.11% 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 4424389 0.01775076419970083 0.26831862483139723 chr2 243199373 4742863 0.01950195406137005 0.23314153535651252 chr3 198022430 3827053 0.019326361160197862 0.1486832520262134 chr4 191154276 3750285 0.019619153065663045 0.1634987962489281 chr5 180915260 3422018 0.01891503237482565 0.14711782388111325 chr6 171115067 3290527 0.01922990802440559 0.15508909972484455 chr7 159138663 3135410 0.019702377416605542 0.2202047410095885 chr8 146364022 2852824 0.019491292744059738 0.18344234133183454 chr9 141213431 2380055 0.016854310409043175 0.15954842301975844 chr10 135534747 2752671 0.020309707000818026 0.1919163542570583 chr11 135006516 2607309 0.019312467851551697 0.1707736097911675 chr12 133851895 2584767 0.01931064928143154 0.15013710176526857 chr13 115169878 1786119 0.015508560319912816 0.132743504263019 chr14 107349540 1728763 0.016104055965214196 0.14078902951213548 chr15 102531392 1659175 0.016182117180268067 0.1380315331065013 chr16 90354753 1676472 0.01855433105992775 0.1505107400430785 chr17 81195210 1581343 0.019475816368970535 0.15732007432912484 chr18 78077248 1508936 0.019326193464195868 0.2419624863313063 chr19 59128983 1049928 0.017756571257110915 0.20113666243944114 chr20 63025520 1232978 0.01956315473478045 0.1511007253838387 chr21 48129895 762342 0.01583926164808795 0.14207834238656378 chr22 51304566 728688 0.014203180278340138 0.12744826343681456 chrMT 16571 19439 1.173073441554523 1.2764066054340868 chrX 155270560 3205677 0.020645748943006324 0.1609538507769531 chrY 59373566 184208 0.0031025254572043053 0.09479462478605874