BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536753.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 22,981,238 number of mapped reads = 22,150,289 (96.38%) number of supplementary alignments = 493 (0%) number of secondary alignments = 0 number of mapped bases = 1,104,640,692 bp number of sequenced bases = 1,104,547,625 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 189,349 duplication rate = 0.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3952 >>>>>>> ACTG content number of A's = 340,493,835 bp (30.83%) number of C's = 210,139,406 bp (19.02%) number of T's = 340,887,669 bp (30.86%) number of G's = 212,581,457 bp (19.25%) number of N's = 445,258 bp (0.04%) GC percentage = 38.27% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 3,908,064 number of insertions = 57,314 mapped reads with insertion percentage = 0.26% number of deletions = 55,862 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.02% >>>>>>> Coverage mean coverageData = 0.3568X std coverageData = 0.6619X There is a 27.45% of reference with a coverageData >= 1X There is a 6.53% of reference with a coverageData >= 2X There is a 1.36% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% 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 84664562 0.3396764335443722 0.6576914785327965 chr2 243199373 102437743 0.42120891076474937 0.7060516117553366 chr3 198022430 85562790 0.43208635506593873 0.7093099816214786 chr4 191154276 92184902 0.48225393608249706 0.7483532557075888 chr5 180915260 79233463 0.4379589814590544 0.7157765801938865 chr6 171115067 74975623 0.4381590955985191 0.7191843089683472 chr7 159138663 63239391 0.3973854612565144 0.6950104260568244 chr8 146364022 61761315 0.4219706055904914 0.7050350345905457 chr9 141213431 46068237 0.3262312704518878 0.6405373979483969 chr10 135534747 47216602 0.3483726722860227 0.6406092467113981 chr11 135006516 49225404 0.36461502347042274 0.6681251707617547 chr12 133851895 51025899 0.38121162946553727 0.6815157051117134 chr13 115169878 46702518 0.4055098330485338 0.7075778230607266 chr14 107349540 35261969 0.3284780633433548 0.6419248441674866 chr15 102531392 29600985 0.28870167879901604 0.6063347833127607 chr16 90354753 19814417 0.2192957906708018 0.5195222497907888 chr17 81195210 17471454 0.21517838305978887 0.5190120182467678 chr18 78077248 33495392 0.42900323535993484 0.7114101157054572 chr19 59128983 7634516 0.1291163083254789 0.3900659280219254 chr20 63025520 16866154 0.26760832754731734 0.5745166824279666 chr21 48129895 14228013 0.29561695490920975 0.6299030099163356 chr22 51304566 5586025 0.1088796852896095 0.36467124682708146 chrMT 16571 918 0.055397984430631826 0.22875543217955568 chrX 155270560 35350255 0.22766875446317705 0.5017110613091276 chrY 59373566 5032145 0.0847539627314957 0.3260884378725678