BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548996.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 = 7,898,191 number of mapped reads = 6,844,605 (86.66%) number of secondary alignments = 0 number of mapped bases = 271,692,735 bp number of sequenced bases = 271,663,136 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 544,135 duplication rate = 7.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3441 >>>>>>> ACTG content number of A's = 81,641,495 bp (30.05%) number of C's = 53,961,573 bp (19.86%) number of T's = 81,767,047 bp (30.1%) number of G's = 54,290,309 bp (19.98%) number of N's = 2,712 bp (0%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 796,266 number of insertions = 8,159 mapped reads with insertion percentage = 0.12% number of deletions = 23,017 mapped reads with deletion percentage = 0.34% homopolymer indels = 43.51% >>>>>>> Coverage mean coverageData = 0.0878X std coverageData = 0.7331X There is a 6.97% of reference with a coverageData >= 1X There is a 1.33% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 21701324 0.08706627856305321 1.201213607668412 chr2 243199373 23754906 0.09767667452004491 0.5231450763162538 chr3 198022430 19368302 0.09780862703280634 0.37277221461893656 chr4 191154276 19163734 0.10025270896895866 0.4151890854760902 chr5 180915260 17619244 0.09738948499977282 0.38102335290529343 chr6 171115067 16428919 0.09601094332622387 0.44168589125759117 chr7 159138663 15111670 0.0949591363602194 0.7709499880603471 chr8 146364022 14468622 0.0988536786724814 2.10188161412938 chr9 141213431 11566301 0.08190652205029987 0.48246975088314253 chr10 135534747 13011801 0.09600343297944106 0.5745895358284578 chr11 135006516 12635553 0.09359217150674416 0.47754885848711426 chr12 133851895 12468821 0.0931538623341866 0.38509047611304376 chr13 115169878 9411690 0.08172006572760283 0.33810795898269225 chr14 107349540 8546020 0.07960928384043378 0.4151143186131761 chr15 102531392 7709763 0.07519417077649741 0.32519987299739533 chr16 90354753 7121727 0.07881961671678744 0.3809151957702707 chr17 81195210 6432705 0.07922517843109218 0.37420212960156085 chr18 78077248 7505579 0.09613016841987054 0.9602158985699989 chr19 59128983 4303678 0.07278457672779523 0.9369880160967342 chr20 63025520 5361664 0.08507131714264317 0.37000826128254705 chr21 48129895 3567380 0.07411983757704022 0.3932320747257363 chr22 51304566 2630226 0.051266898934492496 0.2943217614733183 chrMT 16571 6622 0.39961378311508056 0.7305400916796977 chrX 155270560 9242424 0.05952463879823709 0.38310692997576656 chrY 59373566 2554060 0.04301678629173124 0.47199439041564