BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080817.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,473,689 number of mapped reads = 2,264,655 (91.55%) number of supplementary alignments = 16,753 (0.68%) number of secondary alignments = 0 number of mapped bases = 154,332,777 bp number of sequenced bases = 154,277,867 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,737 duplication rate = 5.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4135 >>>>>>> ACTG content number of A's = 43,641,340 bp (28.29%) number of C's = 28,690,437 bp (18.6%) number of T's = 48,820,470 bp (31.64%) number of G's = 33,103,697 bp (21.46%) number of N's = 21,923 bp (0.01%) GC percentage = 40.05% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,226,064 number of insertions = 11,160 mapped reads with insertion percentage = 0.49% number of deletions = 31,639 mapped reads with deletion percentage = 1.38% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 0.4168X There is a 3.71% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.06% 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% of reference with a coverageData >= 8X There is a 0% 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 20059042 0.08047740029502273 0.8968972067731642 chr2 243199373 11613871 0.0477545269000344 0.3925623094867874 chr3 198022430 8632551 0.04359380399483028 0.2707293288539364 chr4 191154276 9537839 0.0498960274370216 0.2923709268920345 chr5 180915260 12135063 0.06707595036482826 0.3291798312845198 chr6 171115067 11022620 0.06441641985857388 0.4361870085868498 chr7 159138663 10809509 0.0679250962413829 0.38874151156646075 chr8 146364022 6980875 0.047695293587928324 0.47129646261132996 chr9 141213431 5200014 0.036823791923871606 0.2796848780553233 chr10 135534747 6690520 0.04936387271966502 0.4557162369349817 chr11 135006516 5912969 0.04379765640348796 0.28015023637743913 chr12 133851895 5986505 0.04472484308122795 0.27036568765924596 chr13 115169878 6818262 0.0592017819103707 0.31123311305092954 chr14 107349540 3965797 0.03694284111510864 0.25246117915881644 chr15 102531392 3389451 0.0330576902730434 0.23119163195049022 chr16 90354753 3228402 0.03573029522863064 0.2615681914037291 chr17 81195210 3800252 0.04680389397354844 0.28195625184744244 chr18 78077248 1748539 0.022394987589726523 0.3743919603634746 chr19 59128983 2319066 0.03922046147825678 0.5955631460186965 chr20 63025520 2516812 0.039933220701709404 0.25536370635967337 chr21 48129895 2360722 0.04904897465494159 0.2963941496478801 chr22 51304566 667677 0.013013987877804093 0.14077913881159482 chrMT 16571 299757 18.08925230824935 10.189341930439396 chrX 155270560 8265482 0.05323276994685921 0.30118047931855874 chrY 59373566 371180 0.0062516036176772675 0.15371702174080185