BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472484.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 = 35,016,806 number of mapped reads = 34,539,386 (98.64%) number of supplementary alignments = 128,314 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,321,793 number of mapped paired reads (second in pair) = 17,217,593 number of mapped paired reads (both in pair) = 34,309,378 number of mapped paired reads (singletons) = 230,008 number of mapped bases = 3,391,361,709 bp number of sequenced bases = 3,390,926,857 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,154,820 duplication rate = 47.37% >>>>>>> Insert size mean insert size = 27,163.0682 std insert size = 1,619,786.822 median insert size = 234 >>>>>>> Mapping quality mean mapping quality = 55.1587 >>>>>>> ACTG content number of A's = 944,395,399 bp (27.85%) number of C's = 756,181,002 bp (22.3%) number of T's = 937,523,175 bp (27.65%) number of G's = 752,300,822 bp (22.19%) number of N's = 526,459 bp (0.02%) GC percentage = 44.49% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 20,175,536 number of insertions = 182,108 mapped reads with insertion percentage = 0.52% number of deletions = 183,663 mapped reads with deletion percentage = 0.53% homopolymer indels = 45.51% >>>>>>> Coverage mean coverageData = 1.0955X std coverageData = 29.7868X There is a 11% of reference with a coverageData >= 1X There is a 5.09% of reference with a coverageData >= 2X There is a 2.13% of reference with a coverageData >= 3X There is a 1.35% of reference with a coverageData >= 4X There is a 0.85% of reference with a coverageData >= 5X There is a 0.69% of reference with a coverageData >= 6X There is a 0.58% of reference with a coverageData >= 7X There is a 0.53% of reference with a coverageData >= 8X There is a 0.49% of reference with a coverageData >= 9X There is a 0.47% of reference with a coverageData >= 10X There is a 0.45% of reference with a coverageData >= 11X There is a 0.44% of reference with a coverageData >= 12X There is a 0.43% of reference with a coverageData >= 13X There is a 0.42% of reference with a coverageData >= 14X There is a 0.41% of reference with a coverageData >= 15X There is a 0.4% of reference with a coverageData >= 16X There is a 0.39% of reference with a coverageData >= 17X There is a 0.38% of reference with a coverageData >= 18X There is a 0.38% of reference with a coverageData >= 19X There is a 0.37% of reference with a coverageData >= 20X There is a 0.36% of reference with a coverageData >= 21X There is a 0.36% of reference with a coverageData >= 22X There is a 0.35% of reference with a coverageData >= 23X There is a 0.35% of reference with a coverageData >= 24X There is a 0.34% of reference with a coverageData >= 25X There is a 0.34% of reference with a coverageData >= 26X There is a 0.33% of reference with a coverageData >= 27X There is a 0.33% of reference with a coverageData >= 28X There is a 0.33% of reference with a coverageData >= 29X There is a 0.32% of reference with a coverageData >= 30X There is a 0.32% of reference with a coverageData >= 31X There is a 0.31% of reference with a coverageData >= 32X There is a 0.31% of reference with a coverageData >= 33X There is a 0.31% of reference with a coverageData >= 34X There is a 0.3% of reference with a coverageData >= 35X There is a 0.3% of reference with a coverageData >= 36X There is a 0.3% of reference with a coverageData >= 37X There is a 0.29% of reference with a coverageData >= 38X There is a 0.29% of reference with a coverageData >= 39X There is a 0.29% of reference with a coverageData >= 40X There is a 0.28% of reference with a coverageData >= 41X There is a 0.28% of reference with a coverageData >= 42X There is a 0.28% of reference with a coverageData >= 43X There is a 0.28% of reference with a coverageData >= 44X There is a 0.27% of reference with a coverageData >= 45X There is a 0.27% of reference with a coverageData >= 46X There is a 0.27% of reference with a coverageData >= 47X There is a 0.27% of reference with a coverageData >= 48X There is a 0.26% of reference with a coverageData >= 49X There is a 0.26% of reference with a coverageData >= 50X There is a 0.26% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 329534215 1.3220998755305007 37.08005026069198 chr2 243199373 229300633 0.9428504283191552 27.178701734433588 chr3 198022430 396942437 2.004532703694223 40.239038298375554 chr4 191154276 128444661 0.671942389612043 19.591866535894038 chr5 180915260 196512840 1.086214838925141 29.672504791445267 chr6 171115067 248812534 1.4540656083780161 36.606651735475694 chr7 159138663 136531333 0.8579394248146976 22.20788725951114 chr8 146364022 158349410 1.0818875283435434 28.164772856675302 chr9 141213431 239130708 1.6933991781560778 36.38715839938714 chr10 135534747 108616242 0.8013903770374102 25.20436388370512 chr11 135006516 149720843 1.1089897542426768 32.858551627978166 chr12 133851895 164564238 1.2294501919453587 31.949906205398086 chr13 115169878 69681458 0.6050319685152398 18.72868337711814 chr14 107349540 69759499 0.6498350994331229 18.045913938210063 chr15 102531392 88559651 0.8637320655902145 26.84315877205019 chr16 90354753 106790160 1.1818986434504448 26.806910130999583 chr17 81195210 117015420 1.4411616153218891 28.729982351757066 chr18 78077248 57578623 0.7374571270749707 20.884447718305545 chr19 59128983 66129207 1.1183890478887486 31.025728088491405 chr20 63025520 64748166 1.0273325154635773 25.25155042577856 chr21 48129895 19339188 0.40181238708291384 13.857778557570784 chr22 51304566 28905245 0.5634049218933067 15.472245750840251 chrMT 16571 12998 0.7843823547160702 1.799875248853562 chrX 155270560 209715444 1.3506452478821485 40.61854362165964 chrY 59373566 6666556 0.11228154967144806 4.348937816011878