BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549130.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 = 15,044,686 number of mapped reads = 13,234,544 (87.97%) number of secondary alignments = 0 number of mapped bases = 525,572,827 bp number of sequenced bases = 525,523,511 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 799,340 duplication rate = 4.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5998 >>>>>>> ACTG content number of A's = 152,239,153 bp (28.97%) number of C's = 109,573,942 bp (20.85%) number of T's = 154,066,312 bp (29.32%) number of G's = 109,518,382 bp (20.84%) number of N's = 125,722 bp (0.02%) GC percentage = 41.69% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,678,484 number of insertions = 13,047 mapped reads with insertion percentage = 0.1% number of deletions = 39,258 mapped reads with deletion percentage = 0.3% homopolymer indels = 46.69% >>>>>>> Coverage mean coverageData = 0.1698X std coverageData = 0.9666X There is a 11.32% of reference with a coverageData >= 1X There is a 3.56% of reference with a coverageData >= 2X There is a 1.19% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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% 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 43069899 0.17279755944920996 1.8686453732154373 chr2 243199373 44003506 0.180935935225458 0.9083634786987334 chr3 198022430 35166612 0.17758903372713888 0.5860200026020952 chr4 191154276 33390336 0.1746774212887605 0.6026627833092634 chr5 180915260 32193967 0.1779505333049296 0.600209624919181 chr6 171115067 30365766 0.17745816620578478 0.6716217807604492 chr7 159138663 37589559 0.23620632655434587 1.5387850406503514 chr8 146364022 26774797 0.18293291366371445 0.8811396938930953 chr9 141213431 22196873 0.15718669848054326 0.8449289999858789 chr10 135534747 24980458 0.18431035991087955 0.8625714812001288 chr11 135006516 24271037 0.17977678203324646 0.827163112614578 chr12 133851895 23571495 0.17610131705643764 0.6177770369795724 chr13 115169878 16654156 0.14460513711753692 0.5163543056325419 chr14 107349540 15731537 0.1465449875239335 0.7249159738974451 chr15 102531392 15667995 0.1528116871757676 0.5342280974799419 chr16 90354753 14946359 0.16541862496154464 0.633959149230823 chr17 81195210 14343369 0.17665289614990834 0.6379226715984636 chr18 78077248 13767015 0.17632556670030172 1.7369666812449975 chr19 59128983 10833108 0.1832114717751868 1.5727537911892804 chr20 63025520 11335517 0.17985598532150152 0.6385179453265827 chr21 48129895 6856886 0.14246625719835873 0.6212897875706151 chr22 51304566 6453899 0.12579580148870181 0.5243392582911309 chrMT 16571 114663 6.919497918049605 9.692989699347812 chrX 155270560 17099233 0.11012540303841244 0.6046739664379047 chrY 59373566 4194785 0.07065071685268154 0.5593248926093717