BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237260.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 = 3,436,770 number of mapped reads = 2,880,963 (83.83%) number of supplementary alignments = 34,061 (0.99%) number of secondary alignments = 0 number of mapped bases = 178,799,153 bp number of sequenced bases = 178,705,588 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 601,997 duplication rate = 16.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9341 >>>>>>> ACTG content number of A's = 47,031,059 bp (26.32%) number of C's = 30,931,673 bp (17.31%) number of T's = 59,477,644 bp (33.28%) number of G's = 41,246,268 bp (23.08%) number of N's = 18,944 bp (0.01%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,166,660 number of insertions = 15,085 mapped reads with insertion percentage = 0.52% number of deletions = 53,683 mapped reads with deletion percentage = 1.84% homopolymer indels = 42.23% >>>>>>> Coverage mean coverageData = 0.0578X std coverageData = 0.7571X There is a 3.34% of reference with a coverageData >= 1X There is a 1.32% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 20567819 0.0825186269044441 0.7393099961722083 chr2 243199373 13889215 0.05711040628381883 1.2540060858194686 chr3 198022430 10348462 0.05225903954415669 0.3559474800328713 chr4 191154276 10327096 0.05402492801155021 0.595744541940883 chr5 180915260 8162790 0.04511941115415029 0.33438602073311496 chr6 171115067 13349360 0.0780139366687096 0.5726024751480678 chr7 159138663 13151588 0.08264231803933152 0.9219950728149644 chr8 146364022 13349691 0.09120882862866395 1.8264726090599823 chr9 141213431 6853987 0.04853636762072582 0.5190036049772989 chr10 135534747 7721862 0.056973301466376 0.8053763376708145 chr11 135006516 3370958 0.024968854095901563 0.3290873768023911 chr12 133851895 4343848 0.03245264476830903 0.30921473484506473 chr13 115169878 7050108 0.06121486036479087 0.42909459858946086 chr14 107349540 7587060 0.070676222739287 0.4390166714764029 chr15 102531392 3153372 0.030755185689861696 0.3017291479865562 chr16 90354753 5865952 0.06492134398286718 0.4545572962599313 chr17 81195210 4714106 0.05805891751496178 0.42067879324196467 chr18 78077248 5299814 0.06787910864891139 1.325377530347204 chr19 59128983 2000234 0.033828317324517486 0.5696493314817563 chr20 63025520 1764361 0.027994390208918547 0.3140997694739094 chr21 48129895 3813322 0.07922980093765009 0.5472311686795419 chr22 51304566 1784876 0.03478980798707078 0.2846191795893994 chrMT 16571 18440 1.1127873996741295 1.8511142210226192 chrX 155270560 9601344 0.06183621673033188 0.43159289347881585 chrY 59373566 709488 0.011949560179693435 0.485017377692508