BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089605.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 12,146,282 number of mapped reads = 10,260,578 (84.48%) number of supplementary alignments = 380 (0%) number of secondary alignments = 0 number of mapped bases = 483,523,652 bp number of sequenced bases = 483,429,116 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,057,612 duplication rate = 20.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.153 >>>>>>> ACTG content number of A's = 155,103,221 bp (32.08%) number of C's = 91,020,695 bp (18.83%) number of T's = 132,041,658 bp (27.31%) number of G's = 105,246,329 bp (21.77%) number of N's = 17,213 bp (0%) GC percentage = 40.6% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 2,398,624 number of insertions = 19,361 mapped reads with insertion percentage = 0.19% number of deletions = 63,157 mapped reads with deletion percentage = 0.61% homopolymer indels = 46.6% >>>>>>> Coverage mean coverageData = 0.1562X std coverageData = 1.2441X There is a 5.43% of reference with a coverageData >= 1X There is a 2.64% of reference with a coverageData >= 2X There is a 1.66% of reference with a coverageData >= 3X There is a 1.15% of reference with a coverageData >= 4X There is a 0.83% of reference with a coverageData >= 5X There is a 0.63% of reference with a coverageData >= 6X There is a 0.49% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.15% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% 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 38851360 0.15587267082475995 1.2922649017341257 chr2 243199373 41266809 0.1696830402601408 1.3950231755122802 chr3 198022430 32386772 0.16355102803253146 1.2171265388534893 chr4 191154276 33393694 0.1746949882512699 1.290951958754054 chr5 180915260 30013252 0.16589674082772232 1.2064045492461688 chr6 171115067 28209887 0.16485916462283243 1.2722618684224296 chr7 159138663 24789114 0.15577053076033445 1.2351690447115218 chr8 146364022 25218516 0.17229996590282276 1.4600877547360016 chr9 141213431 19883913 0.14080751993059357 1.1333470759260054 chr10 135534747 22027979 0.16252643316624923 1.2444517483471735 chr11 135006516 22133196 0.16394168708123688 1.2941723557503395 chr12 133851895 22241499 0.1661649915378486 1.2066467346801182 chr13 115169878 16286172 0.14140999611026764 1.1323177777557083 chr14 107349540 15093180 0.14059845994682418 1.2421070573078874 chr15 102531392 13287218 0.1295917059235868 1.041721683086099 chr16 90354753 13036168 0.14427761204770267 1.1427951124598272 chr17 81195210 11883227 0.14635379353043115 1.1294648116369312 chr18 78077248 12523563 0.160399646770337 1.269212345330411 chr19 59128983 8390956 0.14190935771717908 1.1816763703224138 chr20 63025520 9601566 0.15234409807328841 1.1747575604673164 chr21 48129895 6233963 0.12952371909392282 1.0984176050304817 chr22 51304566 5194999 0.10125802448070606 0.9383325079506545 chrMT 16571 265537 16.024198901695733 30.670741035153647 chrX 155270560 30113582 0.19394263793471217 1.4042192717413373 chrY 59373566 1197530 0.020169413438970468 0.41595410297818564