BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080742.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 8,133,359 number of mapped reads = 6,618,413 (81.37%) number of supplementary alignments = 42,831 (0.53%) number of secondary alignments = 0 number of mapped bases = 424,899,936 bp number of sequenced bases = 424,761,998 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,276,877 duplication rate = 13.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1728 >>>>>>> ACTG content number of A's = 133,771,505 bp (31.49%) number of C's = 84,687,126 bp (19.94%) number of T's = 109,259,644 bp (25.72%) number of G's = 96,065,672 bp (22.62%) number of N's = 978,051 bp (0.23%) GC percentage = 42.55% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 4,153,231 number of insertions = 29,581 mapped reads with insertion percentage = 0.44% number of deletions = 73,433 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.29% >>>>>>> Coverage mean coverageData = 0.1373X std coverageData = 0.8303X There is a 6.97% of reference with a coverageData >= 1X There is a 2.95% of reference with a coverageData >= 2X There is a 1.48% of reference with a coverageData >= 3X There is a 0.81% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 51672390 0.20731097797345108 1.2506184612029314 chr2 243199373 31955510 0.13139635026937344 0.7376350172488781 chr3 198022430 22782784 0.11505153229358916 0.6141654957307515 chr4 191154276 24322663 0.12724100924637438 0.6998241649401283 chr5 180915260 33081763 0.18285778104069275 0.7903261892774823 chr6 171115067 29382803 0.17171371004985786 0.8702874956731974 chr7 159138663 29266015 0.18390260699877817 1.0882563289175164 chr8 146364022 17805963 0.12165532729074635 1.0423874911990862 chr9 141213431 12880067 0.09120992889125398 0.5887875018696255 chr10 135534747 19379357 0.14298441860078878 0.9729813645805643 chr11 135006516 17470273 0.12940318376929302 0.7511885054936964 chr12 133851895 16673837 0.12456930101736699 0.6456763924713337 chr13 115169878 16794825 0.14582654155455474 0.721742222638261 chr14 107349540 12058753 0.11233166905046822 0.6335582434892679 chr15 102531392 10859408 0.10591300662337638 0.5875646454752784 chr16 90354753 12715050 0.14072364294991765 0.7470436654510222 chr17 81195210 10469516 0.12894253244741902 0.6874498050781308 chr18 78077248 6372491 0.08161777167146055 0.796262449556873 chr19 59128983 7128518 0.12055877910161249 1.3474180604219088 chr20 63025520 6479810 0.10281247977009948 0.5953617208760784 chr21 48129895 6647931 0.13812477671102336 0.7448661469781307 chr22 51304566 2780854 0.054202855940736344 0.4374568019318304 chrMT 16571 28142 1.6982680586566894 2.2041880076572835 chrX 155270560 24701297 0.159085514987516 0.7372785238924705 chrY 59373566 1189916 0.020041174552325187 0.4582564842795095