BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536748.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 17,409,789 number of mapped reads = 14,140,490 (81.22%) number of supplementary alignments = 337 (0%) number of secondary alignments = 0 number of mapped bases = 705,006,488 bp number of sequenced bases = 704,945,598 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,817 duplication rate = 0.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3184 >>>>>>> ACTG content number of A's = 222,229,280 bp (31.52%) number of C's = 129,701,496 bp (18.4%) number of T's = 220,027,414 bp (31.21%) number of G's = 132,972,487 bp (18.86%) number of N's = 14,921 bp (0%) GC percentage = 37.26% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 2,500,215 number of insertions = 46,488 mapped reads with insertion percentage = 0.33% number of deletions = 36,756 mapped reads with deletion percentage = 0.26% homopolymer indels = 48.91% >>>>>>> Coverage mean coverageData = 0.2277X std coverageData = 0.5287X There is a 18.66% of reference with a coverageData >= 1X There is a 3.42% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 52851046 0.21203977662306406 0.5104075788620684 chr2 243199373 66300173 0.27261654576716365 0.5659087222150475 chr3 198022430 58927804 0.29758146084764237 0.5918602506755667 chr4 191154276 62032452 0.32451511573824277 0.6154366294373718 chr5 180915260 52147991 0.28824539732027027 0.5803478723198459 chr6 171115067 47418545 0.2771149603091351 0.625681908699583 chr7 159138663 40379059 0.25373506499800114 0.5521404360364182 chr8 146364022 40082678 0.273856084659931 0.5666900508442322 chr9 141213431 29671606 0.2101188661013413 0.5084456898408928 chr10 135534747 29420002 0.21706612253461469 0.5021591365573885 chr11 135006516 31366786 0.23233534891012222 0.5268340700738763 chr12 133851895 31593782 0.23603537327581353 0.5317217103069516 chr13 115169878 32649542 0.2834902890146328 0.58818749706858 chr14 107349540 21903720 0.20404111652457943 0.4984359066976912 chr15 102531392 17849191 0.174085132873257 0.4724738631777742 chr16 90354753 11658250 0.1290275233224311 0.39312497205819025 chr17 81195210 9211140 0.1134443768296184 0.37016035401867536 chr18 78077248 21839953 0.2797223718745825 0.5795869024620376 chr19 59128983 3435729 0.05810566706347715 0.2562456362793781 chr20 63025520 10874179 0.17253612504902777 0.4565057122471287 chr21 48129895 9327867 0.19380609494369352 0.4994480450669978 chr22 51304566 2753034 0.053660604009397525 0.24744468529671215 chrMT 16571 2336 0.14096916299559473 0.38030507425578003 chrX 155270560 18492358 0.11909764478211453 0.35890275196997007 chrY 59373566 2817265 0.04744981967227638 0.23485147351413446