BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063570.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 = 1,824,012 number of mapped reads = 1,357,844 (74.44%) number of supplementary alignments = 14,248 (0.78%) number of secondary alignments = 0 number of mapped bases = 85,747,189 bp number of sequenced bases = 85,714,702 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 214,632 duplication rate = 11.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4208 >>>>>>> ACTG content number of A's = 23,025,954 bp (26.86%) number of C's = 15,510,071 bp (18.09%) number of T's = 27,543,338 bp (32.13%) number of G's = 19,633,618 bp (22.91%) number of N's = 1,721 bp (0%) GC percentage = 41% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 677,017 number of insertions = 6,493 mapped reads with insertion percentage = 0.47% number of deletions = 20,449 mapped reads with deletion percentage = 1.49% homopolymer indels = 46.49% >>>>>>> Coverage mean coverageData = 0.0277X std coverageData = 0.3666X There is a 1.4% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 7262980 0.029139265414307634 0.5694256256757365 chr2 243199373 7185880 0.02954728012394999 0.48343788774792124 chr3 198022430 5597985 0.028269449072006642 0.2987440417176125 chr4 191154276 5493017 0.028736040411672506 0.32145315967386967 chr5 180915260 5214697 0.028823975379412437 0.3005463769265004 chr6 171115067 4873541 0.028481074667726366 0.33460548883235147 chr7 159138663 4954278 0.03113183123827049 0.40425353140109177 chr8 146364022 4193905 0.028653933819883688 0.3884461019946965 chr9 141213431 3483703 0.02466977096534111 0.3115775491672157 chr10 135534747 4051335 0.029891486055601667 0.3427824630721656 chr11 135006516 3795700 0.028114939281893625 0.3244570592266985 chr12 133851895 3968977 0.029652004553241476 0.30531731815445023 chr13 115169878 2462136 0.02137829823871134 0.25829280483453904 chr14 107349540 2521377 0.02348754358891524 0.28542006120015473 chr15 102531392 2512970 0.02450927419380008 0.3072294555634404 chr16 90354753 2277834 0.02520989681638552 0.2841960405772395 chr17 81195210 2059452 0.025364205597842533 0.3129191908679113 chr18 78077248 2335945 0.029918382881527792 0.4888803074706887 chr19 59128983 1871175 0.031645648294001606 0.4043482211289294 chr20 63025520 1729782 0.027445739440150593 0.2937403909162267 chr21 48129895 1155950 0.024017297357494756 0.2717416143064288 chr22 51304566 897671 0.01749690271232389 0.22025820006251315 chrMT 16571 55529 3.350974594170539 3.317517642579542 chrX 155270560 5533307 0.035636549517178276 0.3440977134065899 chrY 59373566 258063 0.004346429183653884 0.12807260402712312