BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472538.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 = 17,166,650 number of mapped reads = 16,946,620 (98.72%) number of supplementary alignments = 60,311 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,499,013 number of mapped paired reads (second in pair) = 8,447,607 number of mapped paired reads (both in pair) = 16,838,740 number of mapped paired reads (singletons) = 107,880 number of mapped bases = 1,668,169,073 bp number of sequenced bases = 1,667,982,061 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,533,931 duplication rate = 46.82% >>>>>>> Insert size mean insert size = 26,887.7857 std insert size = 1,600,158.3789 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 54.9681 >>>>>>> ACTG content number of A's = 462,671,173 bp (27.74%) number of C's = 373,678,162 bp (22.4%) number of T's = 459,670,315 bp (27.56%) number of G's = 371,703,804 bp (22.28%) number of N's = 258,607 bp (0.02%) GC percentage = 44.69% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 9,905,039 number of insertions = 93,916 mapped reads with insertion percentage = 0.55% number of deletions = 81,381 mapped reads with deletion percentage = 0.48% homopolymer indels = 45.8% >>>>>>> Coverage mean coverageData = 0.5389X std coverageData = 17.7545X There is a 5.15% of reference with a coverageData >= 1X There is a 2.23% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 189878395 0.7617970789328545 25.975810204956222 chr2 243199373 123382256 0.5073296632224459 18.89389409484534 chr3 198022430 190936115 0.9642145841761461 22.43410701217694 chr4 191154276 72270459 0.3780739856428846 14.12972559167165 chr5 180915260 85989089 0.47530036438053924 15.599100703863481 chr6 171115067 92309267 0.5394572705862307 15.34674554644338 chr7 159138663 92433183 0.5808342313394954 21.244767344241044 chr8 146364022 71892341 0.4911886132782003 14.726899070016026 chr9 141213431 93779752 0.664099380178646 16.054042552066456 chr10 135534747 31129759 0.22968102046923805 7.050924216161486 chr11 135006516 73292640 0.542882241328263 14.884633533002475 chr12 133851895 91472153 0.6833833245319388 21.130233129906728 chr13 115169878 34406667 0.29874709948029987 9.96819650908926 chr14 107349540 40859492 0.38062102548366766 12.202732373126246 chr15 102531392 45892183 0.4475915337226671 12.835561615972532 chr16 90354753 57988309 0.6417848212146626 19.321479711733804 chr17 81195210 60472559 0.7447798829512233 22.532892009675404 chr18 78077248 26752983 0.3426476173955312 12.248314665171117 chr19 59128983 32903498 0.5564698787395007 14.16470413855651 chr20 63025520 27141093 0.4306365580164987 11.065897377085319 chr21 48129895 7507036 0.15597449360735152 5.135574749120262 chr22 51304566 18331488 0.35730714494300564 11.139235653117263 chrMT 16571 3371 0.20342767485366 0.5338827542155927 chrX 155270560 105040435 0.6764993634337378 25.861147760520332 chrY 59373566 2104550 0.035445908706241425 1.508228214651638