BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094039.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 392,588 number of mapped reads = 376,978 (96.02%) number of supplementary alignments = 15,149 (3.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 189,437 number of mapped paired reads (second in pair) = 187,541 number of mapped paired reads (both in pair) = 374,124 number of mapped paired reads (singletons) = 2,854 number of mapped bases = 50,237,024 bp number of sequenced bases = 49,001,850 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 356,061 duplication rate = 51.18% >>>>>>> Insert size mean insert size = 648,277.692 std insert size = 7,030,288.6644 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 41.1165 >>>>>>> ACTG content number of A's = 13,583,661 bp (27.72%) number of C's = 10,889,580 bp (22.22%) number of T's = 13,219,391 bp (26.98%) number of G's = 11,308,642 bp (23.08%) number of N's = 576 bp (0%) GC percentage = 45.3% >>>>>>> Mismatches and indels general error rate = 0.0431 number of mismatches = 2,074,354 number of insertions = 30,900 mapped reads with insertion percentage = 8.05% number of deletions = 169,488 mapped reads with deletion percentage = 41.62% homopolymer indels = 29.96% >>>>>>> Coverage mean coverageData = 0.0162X std coverageData = 4.069X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 0.01% 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 0.01% 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 790657 0.003172136530002868 1.4357125377294742 chr2 243199373 1837014 0.007553530987104971 2.5650487033880234 chr3 198022430 900422 0.004547070753550494 1.3192374772668605 chr4 191154276 1040011 0.005440689174015652 2.077878343253535 chr5 180915260 647204 0.0035773875570253165 1.1833721738467846 chr6 171115067 1795881 0.010495165805592094 4.321093138188671 chr7 159138663 1217701 0.007651823743171702 2.4998225987711136 chr8 146364022 1336990 0.009134690217791364 3.216430155954321 chr9 141213431 339278 0.002402590161554817 0.8123446117058976 chr10 135534747 713838 0.0052668265208773365 1.7803791682715393 chr11 135006516 873725 0.006471724668459706 1.939156297003418 chr12 133851895 2808879 0.02098497746333737 5.4054025829612895 chr13 115169878 1100798 0.009558037388908236 2.959748228806709 chr14 107349540 244096 0.0022738429992340907 0.9192684997613316 chr15 102531392 244192 0.002381631568993036 0.7007109147520172 chr16 90354753 285675 0.00316170417731096 1.0081339318980296 chr17 81195210 668381 0.008231778697290148 2.137669534375846 chr18 78077248 265790 0.003404192729743753 0.9432305569544699 chr19 59128983 197290 0.0033366039798113896 0.981269155823768 chr20 63025520 194466 0.0030855120275088566 0.6264311225044137 chr21 48129895 77794 0.0016163342970102054 0.38186988142440026 chr22 51304566 93402 0.001820539715704836 0.3869993724395437 chrMT 16571 3212587 193.86802244885644 786.2357706911881 chrX 155270560 29200719 0.1880634616117827 12.532739123127067 chrY 59373566 150234 0.0025303179532790735 0.7672538544473954