BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238618.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,161,797 number of mapped reads = 943,059 (81.17%) number of supplementary alignments = 6,770 (0.58%) number of secondary alignments = 0 number of mapped bases = 57,652,000 bp number of sequenced bases = 57,620,454 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 319,487 duplication rate = 19.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6354 >>>>>>> ACTG content number of A's = 14,109,498 bp (24.49%) number of C's = 9,908,694 bp (17.2%) number of T's = 19,838,103 bp (34.43%) number of G's = 13,761,570 bp (23.88%) number of N's = 2,589 bp (0%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 390,630 number of insertions = 4,911 mapped reads with insertion percentage = 0.52% number of deletions = 18,058 mapped reads with deletion percentage = 1.89% homopolymer indels = 41.03% >>>>>>> Coverage mean coverageData = 0.0186X std coverageData = 0.4311X There is a 0.78% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 3932807 0.01577852437928329 0.37905989719362876 chr2 243199373 4700020 0.019325789955881176 0.9445182853583941 chr3 198022430 2789736 0.014087979831375668 0.2579989618639875 chr4 191154276 4851107 0.02537796748004737 0.37302660460813913 chr5 180915260 2131749 0.011783135375092185 0.2359153788099272 chr6 171115067 3266116 0.01908724963418914 0.4248165630127254 chr7 159138663 2741532 0.017227315778064568 0.3132579295272364 chr8 146364022 3262011 0.02228697295568989 0.3677634164556784 chr9 141213431 5195194 0.03678965919325337 0.43767423084439916 chr10 135534747 2321266 0.017126722492793674 0.37306702507497014 chr11 135006516 3275671 0.02426305853267112 0.34847393620316075 chr12 133851895 3172677 0.023702891916472308 0.34671313160058476 chr13 115169878 1226771 0.01065183901644838 0.28459987889767846 chr14 107349540 1774324 0.016528473247300363 0.29206531841281586 chr15 102531392 1379077 0.013450290424224418 0.3115950431653847 chr16 90354753 1858962 0.020574036653057976 0.3229088112445517 chr17 81195210 2588710 0.03188254578071785 0.4050401423993678 chr18 78077248 1136454 0.0145555078990489 0.7461836728058944 chr19 59128983 1332852 0.022541432853665014 0.3680495261771703 chr20 63025520 1059921 0.016817330503580138 0.30521010742427757 chr21 48129895 880434 0.018292871821141518 0.34005757211740195 chr22 51304566 449061 0.00875284667645371 0.19746607601255722 chrMT 16571 59340 3.58095467986241 4.7817488031128885 chrX 155270560 2028977 0.013067364476562718 0.23926710023321157 chrY 59373566 237231 0.003995565972911245 0.20164166887908658