BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068062.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 = 2,105,025 number of mapped reads = 1,590,097 (75.54%) number of supplementary alignments = 16,924 (0.8%) number of secondary alignments = 0 number of mapped bases = 98,601,495 bp number of sequenced bases = 98,564,452 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 297,008 duplication rate = 13.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9158 >>>>>>> ACTG content number of A's = 26,117,147 bp (26.5%) number of C's = 18,408,661 bp (18.68%) number of T's = 30,985,351 bp (31.44%) number of G's = 23,051,526 bp (23.39%) number of N's = 1,767 bp (0%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 788,562 number of insertions = 7,091 mapped reads with insertion percentage = 0.44% number of deletions = 23,872 mapped reads with deletion percentage = 1.49% homopolymer indels = 44.84% >>>>>>> Coverage mean coverageData = 0.0319X std coverageData = 0.4028X There is a 1.57% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% 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% 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 9615193 0.038576405392386166 0.47369375580556095 chr2 243199373 8352379 0.03434375219380192 0.6981256105535156 chr3 198022430 4919559 0.024843443240243037 0.2910359897371386 chr4 191154276 7710865 0.040338438466320264 0.3758118058333646 chr5 180915260 4007511 0.02215131548328206 0.27120587618081893 chr6 171115067 8646523 0.05053045971691084 0.45117029696275607 chr7 159138663 4500090 0.02827779192791132 0.33844943625658247 chr8 146364022 4408632 0.030121008836447527 0.4380894448073894 chr9 141213431 2893648 0.020491308648962717 0.2975888628295048 chr10 135534747 12280147 0.0906051567720859 0.5716174041991599 chr11 135006516 2829582 0.020958855052596127 0.2818006097378166 chr12 133851895 2889767 0.02158928717445502 0.2716161827618536 chr13 115169878 3361913 0.029190905281674433 0.32595196731123915 chr14 107349540 2278541 0.02122543794784775 0.3385994478999308 chr15 102531392 1969962 0.019213257145674956 0.3893385266146748 chr16 90354753 1803094 0.01995571832286454 0.2623467691637073 chr17 81195210 3608983 0.044448225455664195 0.390742080429809 chr18 78077248 2698707 0.03456457635392067 0.4033234093117415 chr19 59128983 1912452 0.03234373234526966 0.4191531367335733 chr20 63025520 2124925 0.03371531087724464 0.344089658631006 chr21 48129895 783751 0.016284078741497357 0.23329458679602158 chr22 51304566 646652 0.01260418029849429 0.1909642628336507 chrMT 16571 79501 4.797598213746907 4.05082409614217 chrX 155270560 4072452 0.026228101450783716 0.32580470170569426 chrY 59373566 206666 0.0034807745925181585 0.10340346557931156