BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617503.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,539,059 (95.43%) number of supplementary alignments = 160,113 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,400,475 number of mapped paired reads (second in pair) = 15,138,584 number of mapped paired reads (both in pair) = 30,004,622 number of mapped paired reads (singletons) = 534,437 number of mapped bases = 2,974,277,338 bp number of sequenced bases = 2,972,504,730 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,306,445 duplication rate = 9.99% >>>>>>> Insert size mean insert size = 38,390.0747 std insert size = 1,829,960.4628 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 52.7188 >>>>>>> ACTG content number of A's = 876,313,564 bp (29.48%) number of C's = 600,620,989 bp (20.21%) number of T's = 876,839,728 bp (29.5%) number of G's = 615,782,260 bp (20.72%) number of N's = 2,948,189 bp (0.1%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.012 number of mismatches = 34,685,899 number of insertions = 444,808 mapped reads with insertion percentage = 1.43% number of deletions = 1,037,188 mapped reads with deletion percentage = 3.32% homopolymer indels = 47.47% >>>>>>> Coverage mean coverageData = 0.9608X std coverageData = 9.6995X There is a 38.22% of reference with a coverageData >= 1X There is a 20.64% of reference with a coverageData >= 2X There is a 11.65% of reference with a coverageData >= 3X There is a 6.93% of reference with a coverageData >= 4X There is a 4.28% of reference with a coverageData >= 5X There is a 2.74% of reference with a coverageData >= 6X There is a 1.81% of reference with a coverageData >= 7X There is a 1.24% of reference with a coverageData >= 8X There is a 0.87% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 191305236 0.7675216022831896 9.366242534741389 chr2 243199373 307197841 1.263152273834193 11.465505699537609 chr3 198022430 245985349 1.2422095264662696 2.248853110218729 chr4 191154276 153566105 0.8033621230633627 6.162987074168027 chr5 180915260 190136180 1.0509681715074781 2.080839018431955 chr6 171115067 140208586 0.8193818841212854 5.366214649852383 chr7 159138663 229298483 1.4408722473683218 13.006611697660576 chr8 146364022 132196486 0.9032034252242672 3.862748640648199 chr9 141213431 123461565 0.8742905269400331 18.400733624135206 chr10 135534747 125934546 0.9291679719592497 18.596379446430376 chr11 135006516 167760800 1.2426126158236688 12.838193270347336 chr12 133851895 130233018 0.972963572910193 2.0101087157441357 chr13 115169878 125935228 1.093473659840119 2.13203958134252 chr14 107349540 86512515 0.8058955352766299 2.221795058889078 chr15 102531392 67317596 0.656555955077641 1.496687114570922 chr16 90354753 79966938 0.8850329987621127 14.85661266417885 chr17 81195210 83288197 1.0257772225726123 13.707383547319544 chr18 78077248 53272723 0.6823078984546177 17.112517615807363 chr19 59128983 35552639 0.6012726280105308 5.738408040913224 chr20 63025520 88075323 1.3974549198483408 2.7979755142570855 chr21 48129895 42860335 0.8905137856627362 3.78433052477062 chr22 51304566 22345982 0.4355554240532899 1.2553330276492314 chrMT 16571 2081051 125.58391165288758 93.46157204698943 chrX 155270560 139503890 0.8984567969613815 4.118280815160354 chrY 59373566 10280726 0.17315325139810533 13.64856106145988