BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472596.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 10,265,656 number of mapped reads = 9,524,340 (92.78%) number of supplementary alignments = 307,554 (3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,806,579 number of mapped paired reads (second in pair) = 4,717,761 number of mapped paired reads (both in pair) = 9,313,966 number of mapped paired reads (singletons) = 210,374 number of mapped bases = 775,824,477 bp number of sequenced bases = 775,495,170 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,490,609 duplication rate = 13.53% >>>>>>> Insert size mean insert size = 243,647.1412 std insert size = 4,724,679.6509 median insert size = 129 >>>>>>> Mapping quality mean mapping quality = 50.5237 >>>>>>> ACTG content number of A's = 201,015,895 bp (25.92%) number of C's = 154,692,809 bp (19.95%) number of T's = 231,257,276 bp (29.82%) number of G's = 188,040,216 bp (24.25%) number of N's = 488,974 bp (0.06%) GC percentage = 44.2% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 8,926,814 number of insertions = 72,463 mapped reads with insertion percentage = 0.75% number of deletions = 174,837 mapped reads with deletion percentage = 1.8% homopolymer indels = 42.98% >>>>>>> Coverage mean coverageData = 0.2506X std coverageData = 2.2238X There is a 13.45% of reference with a coverageData >= 1X There is a 6.23% of reference with a coverageData >= 2X There is a 2.29% of reference with a coverageData >= 3X There is a 1.12% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.29% 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 0.06% of reference with a coverageData >= 9X There is a 0.04% 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 0.02% 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 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 47752706 0.19158510341284166 2.779916401504668 chr2 243199373 72258030 0.29711437619536957 3.347218265980331 chr3 198022430 37718521 0.19047600314772423 0.661155076228844 chr4 191154276 35218392 0.1842406706089065 1.2163453455433493 chr5 180915260 35055501 0.19376751856089972 0.7088164440198278 chr6 171115067 48185550 0.281597353434692 1.211316882537169 chr7 159138663 69356009 0.43582123723133204 4.398467250760163 chr8 146364022 36628168 0.25025390461051966 1.8582592791943624 chr9 141213431 25464506 0.18032637419595024 2.520675146287006 chr10 135534747 42212112 0.3114486353820397 2.239543552352398 chr11 135006516 38647652 0.2862650866421884 2.2569277059113246 chr12 133851895 37372852 0.2792104811067486 0.8446074102695876 chr13 115169878 34384657 0.2985559904821641 0.8840785915636316 chr14 107349540 18396065 0.17136603473102913 3.620674555077842 chr15 102531392 21194188 0.20670925837035353 0.7149705922290015 chr16 90354753 27143010 0.30040489402920506 1.2801113275192633 chr17 81195210 23924970 0.2946598697139893 1.7606656054348406 chr18 78077248 16789709 0.21503971297758856 4.0700090280069325 chr19 59128983 12735489 0.21538488155630886 2.0092482763095454 chr20 63025520 26125033 0.4145151519574928 1.2914213666359462 chr21 48129895 11433170 0.23754820159071613 1.0285142814134283 chr22 51304566 7252288 0.14135755480321185 0.5938153008872711 chrMT 16571 148893 8.985154788485909 6.605018195556605 chrX 155270560 48466009 0.3121390751730399 1.3260715297677264 chrY 59373566 1960997 0.033028115575877655 0.9542667114121264