BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506324.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 5,408,233 number of mapped reads = 4,555,665 (84.24%) number of supplementary alignments = 88,619 (1.64%) number of secondary alignments = 0 number of mapped bases = 357,224,810 bp number of sequenced bases = 357,067,766 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 828,630 duplication rate = 12.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5012 >>>>>>> ACTG content number of A's = 100,999,670 bp (28.29%) number of C's = 64,930,389 bp (18.18%) number of T's = 101,608,873 bp (28.46%) number of G's = 89,448,426 bp (25.05%) number of N's = 80,408 bp (0.02%) GC percentage = 43.24% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 2,570,802 number of insertions = 31,887 mapped reads with insertion percentage = 0.68% number of deletions = 77,282 mapped reads with deletion percentage = 1.66% homopolymer indels = 43.92% >>>>>>> Coverage mean coverageData = 0.1154X std coverageData = 0.8345X There is a 6.61% of reference with a coverageData >= 1X There is a 2.36% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.3% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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% 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 26102738 0.10472486646282017 1.24139972840701 chr2 243199373 29257174 0.12030119008571621 0.8867677887122399 chr3 198022430 22391547 0.11307581166436549 0.5462536370617483 chr4 191154276 23374578 0.12228121959458547 0.8636834905728323 chr5 180915260 25166814 0.1391082985481711 0.6186509723773775 chr6 171115067 13312127 0.07779634624460043 0.47561339051756774 chr7 159138663 16080147 0.1010448793326861 0.7333989921121298 chr8 146364022 22644526 0.15471374515794598 1.3334621663505604 chr9 141213431 10451364 0.07401111867326558 0.6778887487569101 chr10 135534747 21085872 0.15557539647010224 1.1611722003453786 chr11 135006516 14811276 0.10970786032283064 0.7547879854781963 chr12 133851895 15957330 0.11921631740813232 0.5794449819470355 chr13 115169878 7109019 0.061726374321591275 0.4026239874145429 chr14 107349540 10388913 0.09677650225608792 0.5514259096720311 chr15 102531392 12552415 0.12242509103943502 0.589736407271403 chr16 90354753 13326609 0.1474920638651959 0.7944566818082864 chr17 81195210 9319678 0.11478113056176589 0.6316169394033333 chr18 78077248 6093994 0.07805082986531492 1.1059421601567567 chr19 59128983 8603032 0.145496025189542 0.9910602289313404 chr20 63025520 9646325 0.15305427071446615 0.6933020518657231 chr21 48129895 6138261 0.12753530835668767 0.8705080843427766 chr22 51304566 4249587 0.08283058081029279 0.49117966343235203 chrMT 16571 12247 0.739062217126305 1.8962865773898865 chrX 155270560 27664936 0.17817244943278365 0.7641478878292286 chrY 59373566 1484301 0.02499935745816581 0.941615400910799