BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549021.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,289,136 number of mapped reads = 7,301,168 (88.08%) number of secondary alignments = 0 number of mapped bases = 289,043,648 bp number of sequenced bases = 289,012,890 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 270,187 duplication rate = 2.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9565 >>>>>>> ACTG content number of A's = 83,322,003 bp (28.83%) number of C's = 60,854,652 bp (21.06%) number of T's = 83,851,744 bp (29.01%) number of G's = 60,981,641 bp (21.1%) number of N's = 2,850 bp (0%) GC percentage = 42.16% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 836,962 number of insertions = 9,114 mapped reads with insertion percentage = 0.12% number of deletions = 23,611 mapped reads with deletion percentage = 0.32% homopolymer indels = 40.58% >>>>>>> Coverage mean coverageData = 0.0934X std coverageData = 0.8477X There is a 7.52% of reference with a coverageData >= 1X There is a 1.33% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.07% 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 0.01% 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 22601045 0.09067598270898591 1.0141657771975192 chr2 243199373 24571387 0.10103392412940143 0.5744295803564365 chr3 198022430 19506099 0.09850449264762583 0.3731522146592582 chr4 191154276 18470015 0.096623603648814 0.38103202933031144 chr5 180915260 18304914 0.10117949143704075 0.3867007227634964 chr6 171115067 16963449 0.09913474773089385 0.4289421711292412 chr7 159138663 16092345 0.10112152946766934 0.8366210568835095 chr8 146364022 15261182 0.10426867061633494 2.919141692837348 chr9 141213431 11947456 0.08460566332390862 0.545736221315639 chr10 135534747 13428211 0.09907578165177082 0.4968185560843203 chr11 135006516 13059996 0.09673604198481797 0.6018400011443273 chr12 133851895 12965420 0.09686392560971961 0.3870826321478973 chr13 115169878 9457012 0.08211358876320074 0.3369609273932657 chr14 107349540 8869103 0.08261891946625947 0.41302634369410574 chr15 102531392 8353051 0.08146822974957757 0.33955974945482253 chr16 90354753 7802106 0.0863497020461115 0.3903307348872625 chr17 81195210 7471433 0.0920181498391346 0.39411090339141336 chr18 78077248 7643666 0.09789876303017238 1.0504459872719007 chr19 59128983 5808291 0.0982308625196547 0.971357678567104 chr20 63025520 5985659 0.09497198912440548 0.38489682661991387 chr21 48129895 3725289 0.07740072983745341 0.372765632010892 chr22 51304566 3114169 0.06069964610947104 0.3276912964693898 chrMT 16571 10671 0.6439563092148934 1.0668710705328057 chrX 155270560 16728216 0.10773591593924824 0.47928087798878877 chrY 59373566 903463 0.015216586451957425 0.17636550411820687