BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231761.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 = 4,013,615 number of mapped reads = 3,433,921 (85.56%) number of supplementary alignments = 24,311 (0.61%) number of secondary alignments = 0 number of mapped bases = 226,154,941 bp number of sequenced bases = 226,056,240 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 198,814 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.7969 >>>>>>> ACTG content number of A's = 62,416,371 bp (27.61%) number of C's = 43,864,131 bp (19.4%) number of T's = 65,820,226 bp (29.12%) number of G's = 53,940,118 bp (23.86%) number of N's = 15,394 bp (0.01%) GC percentage = 43.27% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 1,525,020 number of insertions = 17,243 mapped reads with insertion percentage = 0.5% number of deletions = 58,044 mapped reads with deletion percentage = 1.67% homopolymer indels = 44.03% >>>>>>> Coverage mean coverageData = 0.0731X std coverageData = 6.8216X There is a 6.06% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% 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 20441032 0.08200995414972306 2.0641280265483823 chr2 243199373 20922947 0.08603207624223604 24.14326605529231 chr3 198022430 20723161 0.10465057417990477 0.3725845939254852 chr4 191154276 9695440 0.050720497615235144 0.32079030868343755 chr5 180915260 9696581 0.05359736376024886 0.2833519093529686 chr6 171115067 18617271 0.10879971779457621 0.6149137822388824 chr7 159138663 13622277 0.08560004679692451 1.5227052335196025 chr8 146364022 11981050 0.08185788991231739 0.9642424755525217 chr9 141213431 11500659 0.08144167958074752 0.6919991614169184 chr10 135534747 8930871 0.06589358963425077 0.7448868794160811 chr11 135006516 8810674 0.06526110191599938 0.5201354213653713 chr12 133851895 7486095 0.0559281958615528 0.2944117438969599 chr13 115169878 7862198 0.06826609645275478 0.2929034702624582 chr14 107349540 7843235 0.07306258601573887 0.48093018318638747 chr15 102531392 3648515 0.03558437010198789 0.23767047713247463 chr16 90354753 5521429 0.06110834036589088 0.44782147924315263 chr17 81195210 5000935 0.06159150274997749 0.3339420023958891 chr18 78077248 4277077 0.05478006858028603 1.5322884027806227 chr19 59128983 5546089 0.09379645511575939 1.3305229623671984 chr20 63025520 4412268 0.07000764134909161 0.3470291274185254 chr21 48129895 4206503 0.08739896482217549 0.3856572068189122 chr22 51304566 2105183 0.04103305347130312 0.22764668958776338 chrMT 16571 273357 16.49610765795667 9.816990707938496 chrX 155270560 12371771 0.07967879422860329 0.4250485641238558 chrY 59373566 658323 0.011087813051350159 0.2224877836070502