BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124882.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 2,548,150 number of mapped reads = 2,503,078 (98.23%) number of supplementary alignments = 37,934 (1.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,252,972 number of mapped paired reads (second in pair) = 1,250,106 number of mapped paired reads (both in pair) = 2,491,278 number of mapped paired reads (singletons) = 11,800 number of mapped bases = 333,580,963 bp number of sequenced bases = 333,311,187 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 403,603 duplication rate = 14.91% >>>>>>> Insert size mean insert size = 92,207.7653 std insert size = 2,892,631.9493 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 53.3371 >>>>>>> ACTG content number of A's = 96,281,693 bp (28.89%) number of C's = 67,312,069 bp (20.19%) number of T's = 97,673,318 bp (29.3%) number of G's = 72,016,617 bp (21.61%) number of N's = 27,490 bp (0.01%) GC percentage = 41.8% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 3,786,254 number of insertions = 65,904 mapped reads with insertion percentage = 2.47% number of deletions = 133,288 mapped reads with deletion percentage = 5.1% homopolymer indels = 45.65% >>>>>>> Coverage mean coverageData = 0.1078X std coverageData = 1.3851X There is a 5.96% of reference with a coverageData >= 1X There is a 3.29% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 25127625 0.10081268764421654 1.3524035346020897 chr2 243199373 27534947 0.11321964633519019 2.105564372206615 chr3 198022430 33481461 0.16907913411627157 0.615656736551257 chr4 191154276 18703861 0.09784694013331934 0.8376134134028753 chr5 180915260 18559207 0.10258508320414762 0.4668580994011781 chr6 171115067 19129822 0.11179507646746269 0.7640230595515578 chr7 159138663 16745334 0.10522480008519362 1.4523330490164834 chr8 146364022 22420195 0.1531810529229649 0.7311545874725907 chr9 141213431 10573750 0.07487779260883477 1.799632610582182 chr10 135534747 20483479 0.15113083141697975 3.876641155648238 chr11 135006516 15467006 0.11456488514969158 0.7942832163378971 chr12 133851895 15089694 0.11273425751648865 0.4760044915739664 chr13 115169878 5926170 0.051455902384475914 0.3167496548841733 chr14 107349540 12458505 0.11605550429000441 0.5067113770797843 chr15 102531392 6384321 0.062266988436087946 0.349995174471893 chr16 90354753 9768598 0.10811382551175808 1.7551122855153438 chr17 81195210 9433985 0.11618893528325132 1.1262812525774903 chr18 78077248 7037158 0.09013071259888668 1.7922060051408943 chr19 59128983 4778210 0.08080994729775752 0.8528291040525128 chr20 63025520 8450606 0.13408228920602322 0.5640179182642432 chr21 48129895 3997260 0.08305150052789435 0.6241287633956236 chr22 51304566 2436455 0.047490022622937694 0.33298154127187385 chrMT 16571 283608 17.114718484098727 10.845723915238567 chrX 155270560 14690671 0.09461337036460743 0.5407705367177601 chrY 59373566 4619035 0.07779615258413146 1.8687116062190463