BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506330.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 = 7,345,009 number of mapped reads = 5,400,227 (73.52%) number of supplementary alignments = 94,347 (1.28%) number of secondary alignments = 0 number of mapped bases = 407,859,093 bp number of sequenced bases = 407,675,622 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 592,969 duplication rate = 7.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7156 >>>>>>> ACTG content number of A's = 113,619,835 bp (27.87%) number of C's = 73,685,113 bp (18.07%) number of T's = 114,384,820 bp (28.06%) number of G's = 105,889,201 bp (25.97%) number of N's = 96,653 bp (0.02%) GC percentage = 44.05% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 3,035,855 number of insertions = 37,263 mapped reads with insertion percentage = 0.67% number of deletions = 88,298 mapped reads with deletion percentage = 1.6% homopolymer indels = 42.42% >>>>>>> Coverage mean coverageData = 0.1318X std coverageData = 0.845X There is a 9.05% of reference with a coverageData >= 1X There is a 2.32% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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% 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 30027173 0.12046980215948991 1.1821321525519426 chr2 243199373 33060024 0.13593794914923568 0.9690319916678198 chr3 198022430 25082939 0.1266671608867743 0.48921919026497035 chr4 191154276 24720900 0.1293243369559779 1.0160443411328908 chr5 180915260 30326222 0.1676266667610018 0.580461393668771 chr6 171115067 15387759 0.08992638269545253 0.45273301362506646 chr7 159138663 21113590 0.13267416982132116 0.8938698965301524 chr8 146364022 24967026 0.17058171577165324 1.2113806227515302 chr9 141213431 11037738 0.07816351406404112 0.643175917082788 chr10 135534747 23963820 0.17680941994896704 1.2138532213787332 chr11 135006516 18182487 0.13467858840235533 0.7482591186662341 chr12 133851895 17362963 0.12971772271135945 0.5188703667191951 chr13 115169878 8278037 0.07187675409363549 0.3622732838569108 chr14 107349540 11686901 0.10886773245604965 0.5178738495926113 chr15 102531392 14536895 0.14177994384393025 0.5530326885727802 chr16 90354753 15791646 0.1747738273381147 0.8301379028720509 chr17 81195210 10538445 0.12979146183623394 0.5778726496867548 chr18 78077248 7154383 0.09163211029159224 1.0870456440852434 chr19 59128983 10654032 0.18018290624075167 1.0057068096260404 chr20 63025520 11247438 0.17845847206020674 0.7005628291727769 chr21 48129895 7017832 0.14581024953409932 0.8936799549852718 chr22 51304566 4982033 0.0971070099296815 0.4622045007060193 chrMT 16571 162062 9.779856375595921 7.356801530194714 chrX 155270560 28722901 0.1849861364575487 0.6865936173161307 chrY 59373566 1853847 0.031223440411175574 1.3308820757330648