BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549071.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 = 9,309,583 number of mapped reads = 8,064,626 (86.63%) number of secondary alignments = 0 number of mapped bases = 320,209,420 bp number of sequenced bases = 320,177,143 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 290,349 duplication rate = 2.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9028 >>>>>>> ACTG content number of A's = 95,033,579 bp (29.68%) number of C's = 64,867,019 bp (20.26%) number of T's = 95,294,902 bp (29.76%) number of G's = 64,975,799 bp (20.29%) number of N's = 5,844 bp (0%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,015,956 number of insertions = 8,298 mapped reads with insertion percentage = 0.1% number of deletions = 25,497 mapped reads with deletion percentage = 0.32% homopolymer indels = 44.34% >>>>>>> Coverage mean coverageData = 0.1034X std coverageData = 0.9773X There is a 8.65% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% 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 26168193 0.10498747363201154 2.324236751237785 chr2 243199373 27834507 0.11445139293183951 0.6194878246938176 chr3 198022430 22604865 0.11415305326775356 0.3887854964756496 chr4 191154276 22341700 0.1168778458296167 0.41144659365003133 chr5 180915260 20672031 0.11426361159362676 0.39543329137967026 chr6 171115067 19491765 0.11391027886515687 0.4727520348802885 chr7 159138663 18072770 0.11356617970329436 0.8805483461091221 chr8 146364022 17141519 0.11711565974867785 2.0898148814227655 chr9 141213431 13534875 0.09584693824201466 0.6040708974384125 chr10 135534747 15093823 0.1113649697520002 0.7255017814659669 chr11 135006516 14794618 0.10958447368569973 0.559256765072438 chr12 133851895 14776578 0.11039498544267902 0.4091840756352038 chr13 115169878 10919975 0.09481624179544586 0.345468401419397 chr14 107349540 9983362 0.09299864722289448 0.4184686968531274 chr15 102531392 9095983 0.08871412766930932 0.33674445215860027 chr16 90354753 8402247 0.09299175440167491 0.4202188765177259 chr17 81195210 7720477 0.09508537511018199 0.4066917853702364 chr18 78077248 8825222 0.11303192960899441 1.2026620878333412 chr19 59128983 5523313 0.09341126330550958 1.80918514472494 chr20 63025520 6322871 0.1003223932146851 0.3767352785126151 chr21 48129895 4169002 0.08661980251567139 0.40934058259137174 chr22 51304566 3124851 0.06090785369863571 0.3295762621759175 chrMT 16571 19607 1.183211634783658 1.5606178536762632 chrX 155270560 10944990 0.0704897953610781 0.4105453443930266 chrY 59373566 2630276 0.0443004551890988 0.3812731424472427