BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819010.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,030,017 number of mapped reads = 1,994,941 (98.27%) number of supplementary alignments = 30,894 (1.52%) number of secondary alignments = 0 number of mapped bases = 184,471,775 bp number of sequenced bases = 184,357,311 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 846,655 duplication rate = 35.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1421 >>>>>>> ACTG content number of A's = 52,623,054 bp (28.54%) number of C's = 39,328,008 bp (21.33%) number of T's = 52,382,755 bp (28.41%) number of G's = 40,014,434 bp (21.7%) number of N's = 9,060 bp (0%) GC percentage = 43.04% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,171,033 number of insertions = 27,034 mapped reads with insertion percentage = 1.31% number of deletions = 59,439 mapped reads with deletion percentage = 2.91% homopolymer indels = 41.05% >>>>>>> Coverage mean coverageData = 0.0596X std coverageData = 0.7461X There is a 2.91% of reference with a coverageData >= 1X There is a 1.32% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.07% 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 0.01% 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 0.01% 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 18772647 0.07531634996407893 1.2618537916352663 chr2 243199373 14113194 0.058031374941085886 1.2017846844495066 chr3 198022430 10923641 0.05516365494555339 0.4158321895658206 chr4 191154276 9792960 0.05123066145797335 0.4944154450165107 chr5 180915260 9698577 0.05360839654985434 0.44487561333069847 chr6 171115067 7141061 0.0417325085698035 0.46469670539338276 chr7 159138663 9475572 0.05954286545690032 0.8050505874872813 chr8 146364022 16922506 0.11561930157945509 0.6707483883176784 chr9 141213431 7807843 0.05529107921752854 0.6870916600292888 chr10 135534747 10147747 0.07487192195813816 0.9452803200100632 chr11 135006516 6312081 0.046753898900701946 0.4729511735051406 chr12 133851895 8044563 0.06010047896594964 0.44346869402738753 chr13 115169878 4010034 0.034818427089069244 0.32709417912840283 chr14 107349540 4219025 0.03930175201495973 0.3793639045252604 chr15 102531392 4806019 0.0468736345645244 0.3854988610098065 chr16 90354753 5881902 0.06509787039094667 0.9870018144437754 chr17 81195210 6407542 0.07891527098704468 0.5689305137110903 chr18 78077248 4449776 0.05699196774968298 0.7546162395037966 chr19 59128983 3818429 0.06457795832544591 1.1105515046535084 chr20 63025520 5520301 0.08758834516557737 0.5700943590874659 chr21 48129895 2584117 0.05369047657386329 0.465800486071845 chr22 51304566 1571327 0.030627429925047998 0.3630524129550752 chrMT 16571 19790 1.1942550238368235 1.971944502951489 chrX 155270560 11261795 0.07253013707170246 0.5665115310242721 chrY 59373566 769326 0.012957382414928557 0.8697830150225999