BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777244.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 49,368,012 number of mapped reads = 49,144,711 (99.55%) number of supplementary alignments = 672,757 (1.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 24,571,227 number of mapped paired reads (second in pair) = 24,573,484 number of mapped paired reads (both in pair) = 49,078,168 number of mapped paired reads (singletons) = 66,543 number of mapped bases = 4,934,019,417 bp number of sequenced bases = 4,933,289,230 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,530,294 duplication rate = 41.5% >>>>>>> Insert size mean insert size = 674,390.0364 std insert size = 8,288,431.9321 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 54.3347 >>>>>>> ACTG content number of A's = 1,241,244,774 bp (25.16%) number of C's = 1,218,315,981 bp (24.7%) number of T's = 1,229,831,562 bp (24.93%) number of G's = 1,243,836,387 bp (25.21%) number of N's = 60,526 bp (0%) GC percentage = 49.91% >>>>>>> Mismatches and indels general error rate = 0.0022 number of mismatches = 10,074,384 number of insertions = 231,166 mapped reads with insertion percentage = 0.46% number of deletions = 307,216 mapped reads with deletion percentage = 0.61% homopolymer indels = 44.59% >>>>>>> Coverage mean coverageData = 1.5938X std coverageData = 10.7673X There is a 20.6% of reference with a coverageData >= 1X There is a 10.89% of reference with a coverageData >= 2X There is a 6.54% of reference with a coverageData >= 3X There is a 4.81% of reference with a coverageData >= 4X There is a 3.93% of reference with a coverageData >= 5X There is a 3.5% of reference with a coverageData >= 6X There is a 3.2% of reference with a coverageData >= 7X There is a 3.01% of reference with a coverageData >= 8X There is a 2.85% of reference with a coverageData >= 9X There is a 2.72% of reference with a coverageData >= 10X There is a 2.61% of reference with a coverageData >= 11X There is a 2.51% of reference with a coverageData >= 12X There is a 2.42% of reference with a coverageData >= 13X There is a 2.33% of reference with a coverageData >= 14X There is a 2.25% of reference with a coverageData >= 15X There is a 2.18% of reference with a coverageData >= 16X There is a 2.11% of reference with a coverageData >= 17X There is a 2.04% of reference with a coverageData >= 18X There is a 1.98% of reference with a coverageData >= 19X There is a 1.92% of reference with a coverageData >= 20X There is a 1.86% of reference with a coverageData >= 21X There is a 1.81% of reference with a coverageData >= 22X There is a 1.76% of reference with a coverageData >= 23X There is a 1.7% of reference with a coverageData >= 24X There is a 1.66% of reference with a coverageData >= 25X There is a 1.61% of reference with a coverageData >= 26X There is a 1.56% of reference with a coverageData >= 27X There is a 1.52% of reference with a coverageData >= 28X There is a 1.48% of reference with a coverageData >= 29X There is a 1.44% of reference with a coverageData >= 30X There is a 1.4% of reference with a coverageData >= 31X There is a 1.36% of reference with a coverageData >= 32X There is a 1.33% of reference with a coverageData >= 33X There is a 1.29% of reference with a coverageData >= 34X There is a 1.26% of reference with a coverageData >= 35X There is a 1.22% of reference with a coverageData >= 36X There is a 1.19% of reference with a coverageData >= 37X There is a 1.16% of reference with a coverageData >= 38X There is a 1.13% of reference with a coverageData >= 39X There is a 1.1% of reference with a coverageData >= 40X There is a 1.07% of reference with a coverageData >= 41X There is a 1.04% of reference with a coverageData >= 42X There is a 1.02% of reference with a coverageData >= 43X There is a 0.99% of reference with a coverageData >= 44X There is a 0.96% of reference with a coverageData >= 45X There is a 0.94% of reference with a coverageData >= 46X There is a 0.91% of reference with a coverageData >= 47X There is a 0.89% of reference with a coverageData >= 48X There is a 0.87% of reference with a coverageData >= 49X There is a 0.85% of reference with a coverageData >= 50X There is a 0.83% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 490724231 1.968798428791076 12.432780810077132 chr2 243199373 385836196 1.5865016066468232 10.138511284134536 chr3 198022430 263225772 1.3292725071599212 8.941399371747375 chr4 191154276 175275750 0.9169334511774144 6.888555672397378 chr5 180915260 224690779 1.2419669794576753 8.317440383092528 chr6 171115067 213663282 1.248652650791996 8.868432709697684 chr7 159138663 317139551 1.9928504175003656 15.406485007795045 chr8 146364022 148174283 1.0123682102695974 7.781856635890224 chr9 141213431 183909968 1.302354646421699 9.045159910582491 chr10 135534747 199282483 1.4703423838611658 9.637858494530688 chr11 135006516 356108963 2.6377168565700932 16.21208874281045 chr12 133851895 258902191 1.9342437475390244 10.86023875674392 chr13 115169878 117123971 1.0169670493182255 8.415648434842597 chr14 107349540 106447385 0.9915960981295309 6.517386008014119 chr15 102531392 227692759 2.2207126476933037 13.789928332727724 chr16 90354753 209623728 2.320007758750666 12.186597082011412 chr17 81195210 274667725 3.382807003023947 15.868947755221392 chr18 78077248 63918521 0.8186574531930224 6.303363644470318 chr19 59128983 307357381 5.198083332500408 20.282104399225982 chr20 63025520 159553041 2.531562468663487 13.890062945677203 chr21 48129895 36296531 0.7541369246702075 8.76203385504965 chr22 51304566 89184756 1.7383395466204703 10.164499510410408 chrMT 16571 1133871 68.4250196125762 23.818349512017583 chrX 155270560 120546722 0.7763656033700143 5.874723274813896 chrY 59373566 3539577 0.05961536822632483 2.3921046479806454