BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716948.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 = 1,241,837 number of mapped reads = 1,053,862 (84.86%) number of supplementary alignments = 5,200 (0.42%) number of secondary alignments = 0 number of mapped bases = 60,734,533 bp number of sequenced bases = 60,717,955 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,566 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9263 >>>>>>> ACTG content number of A's = 15,035,811 bp (24.76%) number of C's = 11,632,056 bp (19.16%) number of T's = 19,221,619 bp (31.66%) number of G's = 14,827,658 bp (24.42%) number of N's = 811 bp (0%) GC percentage = 43.58% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 301,377 number of insertions = 3,901 mapped reads with insertion percentage = 0.37% number of deletions = 10,449 mapped reads with deletion percentage = 0.99% homopolymer indels = 42.93% >>>>>>> Coverage mean coverageData = 0.0196X std coverageData = 0.2137X There is a 1.8% 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 6739081 0.02703736894601358 0.4316712063396316 chr2 243199373 5633659 0.023164776004582874 0.2682864580113156 chr3 198022430 4095984 0.020684444686392345 0.15309657833134205 chr4 191154276 2672430 0.013980487676875196 0.13112423757499175 chr5 180915260 2584236 0.014284234508465455 0.1292714594260979 chr6 171115067 4074218 0.02380981447998381 0.1786260063283467 chr7 159138663 4381026 0.0275296142207755 0.2820384736709516 chr8 146364022 3420812 0.02337194587341963 0.179667905450308 chr9 141213431 2453428 0.017373899795692947 0.170594582737118 chr10 135534747 3154239 0.02327254869926455 0.19446425135067794 chr11 135006516 1937638 0.014352181342121295 0.16378630160539173 chr12 133851895 2404258 0.01796207666690113 0.14496825515582148 chr13 115169878 1332442 0.011569361912495904 0.1146875762388819 chr14 107349540 1295477 0.012067839321901147 0.1255364955342807 chr15 102531392 1795933 0.017515933071502628 0.1436041557280335 chr16 90354753 1266482 0.014016772310804722 0.1337622498692694 chr17 81195210 1333436 0.01642259438703342 0.1389199900812273 chr18 78077248 2072113 0.02653926787993347 0.2819382513404055 chr19 59128983 1527872 0.025839646185018945 0.2781009141831028 chr20 63025520 914700 0.014513168633912105 0.12964141439323543 chr21 48129895 749127 0.015564692173128572 0.13722938527896625 chr22 51304566 952016 0.018556165156918002 0.14483133323873412 chrMT 16571 44202 2.667431054251403 2.00469474914728 chrX 155270560 3765473 0.02425104282486004 0.18140607143656107 chrY 59373566 134251 0.0022611240834010207 0.06242501411451911