BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234056.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,469,253 number of mapped reads = 988,556 (67.28%) number of supplementary alignments = 12,615 (0.86%) number of secondary alignments = 0 number of mapped bases = 62,676,489 bp number of sequenced bases = 62,632,601 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,525 duplication rate = 10% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8414 >>>>>>> ACTG content number of A's = 16,894,255 bp (26.97%) number of C's = 11,179,422 bp (17.85%) number of T's = 20,378,868 bp (32.54%) number of G's = 14,164,931 bp (22.62%) number of N's = 15,125 bp (0.02%) GC percentage = 40.47% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 526,584 number of insertions = 4,757 mapped reads with insertion percentage = 0.48% number of deletions = 25,371 mapped reads with deletion percentage = 2.53% homopolymer indels = 43.93% >>>>>>> Coverage mean coverageData = 0.0202X std coverageData = 0.2679X There is a 1.26% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 5541507 0.022232670786404982 0.4066847970614888 chr2 243199373 2836187 0.011661983191050414 0.2961094994513394 chr3 198022430 5680483 0.028686058442975376 0.2510053510491694 chr4 191154276 2831153 0.014810827459596039 0.1814431334191556 chr5 180915260 4218561 0.0233178837429192 0.22721911740744152 chr6 171115067 4367522 0.02552388913829546 0.265694338682 chr7 159138663 4045195 0.02541930995109592 0.2974814023674928 chr8 146364022 3360757 0.022961633289907815 0.3627254999626978 chr9 141213431 1993754 0.014118727842537867 0.1859124003526436 chr10 135534747 3435083 0.02534466678127934 0.26372584740594507 chr11 135006516 4175939 0.030931388526461937 0.3583179695963054 chr12 133851895 1989557 0.014863868755836441 0.17818302437769445 chr13 115169878 3215632 0.027920772825686245 0.252685357728625 chr14 107349540 3001728 0.02796218782120538 0.2543610954558747 chr15 102531392 778516 0.007592952605188468 0.12729011600954737 chr16 90354753 1577546 0.01745946890032448 0.20075383079194456 chr17 81195210 1477896 0.01820176337988411 0.22339823204346215 chr18 78077248 1009737 0.012932538298481013 0.29941106460254396 chr19 59128983 1020037 0.017251049286607888 0.2880725118279836 chr20 63025520 1378489 0.02187191791515564 0.22538800423247385 chr21 48129895 1221720 0.02538380771451922 0.2379409968029442 chr22 51304566 381624 0.0074384022661842615 0.12279464676761166 chrMT 16571 72131 4.352845332206868 4.201114193892859 chrX 155270560 2893135 0.018632862533631618 0.20983650744610605 chrY 59373566 172600 0.0029070175774855767 0.07468880633389087