BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818997.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 = 2,865,374 number of mapped reads = 2,594,773 (90.56%) number of supplementary alignments = 36,301 (1.27%) number of secondary alignments = 0 number of mapped bases = 240,390,337 bp number of sequenced bases = 240,247,751 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,288,062 duplication rate = 41.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2007 >>>>>>> ACTG content number of A's = 70,024,104 bp (29.15%) number of C's = 49,307,527 bp (20.52%) number of T's = 67,928,001 bp (28.27%) number of G's = 52,976,133 bp (22.05%) number of N's = 11,986 bp (0%) GC percentage = 42.57% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,479,437 number of insertions = 32,719 mapped reads with insertion percentage = 1.22% number of deletions = 75,657 mapped reads with deletion percentage = 2.85% homopolymer indels = 42.49% >>>>>>> Coverage mean coverageData = 0.0777X std coverageData = 0.9446X There is a 3.16% of reference with a coverageData >= 1X There is a 1.68% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% 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% 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 24511244 0.09833975097698955 1.7169019934581349 chr2 243199373 19656087 0.08082293452294385 1.2947189416849418 chr3 198022430 14754568 0.07450957954611505 0.5503247848059141 chr4 191154276 13260502 0.0693706794191724 0.6156144862109836 chr5 180915260 12869202 0.07113386676170932 0.5546568274685193 chr6 171115067 10212048 0.05967942028155826 0.6303017901793896 chr7 159138663 10101509 0.06347614595706387 1.111350052348377 chr8 146364022 22632775 0.15463345903407874 0.9058511825013146 chr9 141213431 10417769 0.07377321637344822 0.8956962353553811 chr10 135534747 12167189 0.08977173211530767 1.1793961665665884 chr11 135006516 7509417 0.05562262639234391 0.5739908938378095 chr12 133851895 11239662 0.08397088438680678 0.606894215365102 chr13 115169878 5196990 0.045124559392170235 0.42796985914456603 chr14 107349540 5749456 0.05355827328184173 0.4942581928294718 chr15 102531392 6262432 0.06107819154547321 0.49641572218797136 chr16 90354753 7440236 0.08234471074255496 1.0793780873489656 chr17 81195210 8238489 0.10146520958563934 0.7399919914231587 chr18 78077248 5294471 0.06781067642138207 1.0299418921463486 chr19 59128983 4919462 0.08319882653824776 1.5242593669493574 chr20 63025520 7098961 0.11263629399646366 0.7503917288953126 chr21 48129895 3374241 0.07010696782114317 0.5943407979471467 chr22 51304566 1925574 0.03753221496893668 0.42015642128168423 chrMT 16571 56915 3.4346146883109046 4.431773116585007 chrX 155270560 14589797 0.09396370438800504 0.7402343387490764 chrY 59373566 911341 0.015349271761780319 1.0068818380582005