BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524514.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 = 2,977,288 number of mapped reads = 2,724,963 (91.53%) number of supplementary alignments = 13,128 (0.44%) number of secondary alignments = 0 number of mapped bases = 158,870,756 bp number of sequenced bases = 158,823,114 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 293,380 duplication rate = 7.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7199 >>>>>>> ACTG content number of A's = 37,614,994 bp (23.68%) number of C's = 32,805,388 bp (20.66%) number of T's = 50,722,429 bp (31.94%) number of G's = 37,678,040 bp (23.72%) number of N's = 2,263 bp (0%) GC percentage = 44.38% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 819,830 number of insertions = 9,643 mapped reads with insertion percentage = 0.35% number of deletions = 28,230 mapped reads with deletion percentage = 1.03% homopolymer indels = 44.39% >>>>>>> Coverage mean coverageData = 0.0513X std coverageData = 0.481X There is a 3.83% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.23% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 15668916 0.06286410014601328 0.9297490743573505 chr2 243199373 12295269 0.0505563351102883 0.6058813235512217 chr3 198022430 8449349 0.04266864617306231 0.2661020931140725 chr4 191154276 8802491 0.04604914514180159 0.3768817540419592 chr5 180915260 8542078 0.04721590649677645 0.28083968010955673 chr6 171115067 6520867 0.038108081972699694 0.3118610283465813 chr7 159138663 7785686 0.04892391234932016 0.5600842303520985 chr8 146364022 14317558 0.09782156710615673 0.530430412633265 chr9 141213431 6700908 0.04745234183850402 0.38850268632035295 chr10 135534747 8336096 0.06150523156987927 0.5382654481798489 chr11 135006516 5634777 0.04173707437943217 0.406467883234446 chr12 133851895 7345079 0.05487467323492133 0.30441947819758053 chr13 115169878 3485760 0.030266247221343762 0.22405706369983122 chr14 107349540 3849000 0.035854834589882735 0.2538097444478976 chr15 102531392 4381868 0.0427368429758566 0.265517456239148 chr16 90354753 4923761 0.054493657904194595 0.3301952533587645 chr17 81195210 5898509 0.07264602185276693 0.3772839239991371 chr18 78077248 3775479 0.0483556874340653 0.7183553334926165 chr19 59128983 3435290 0.05809824261648471 0.6459316518269235 chr20 63025520 4757179 0.07548020230535187 0.3642498530830104 chr21 48129895 2305802 0.04790789591375589 0.34311282853703223 chr22 51304566 1435341 0.027976866620409574 0.2154193297183443 chrMT 16571 192724 11.630197332689638 7.693146012027199 chrX 155270560 9411838 0.0606157277979805 0.35191400882361856 chrY 59373566 619131 0.010427721319618902 0.3439519174521902