BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617405.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 = 30,501,882 (95.32%) number of supplementary alignments = 504,213 (1.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,358,864 number of mapped paired reads (second in pair) = 15,143,018 number of mapped paired reads (both in pair) = 30,019,720 number of mapped paired reads (singletons) = 482,162 number of mapped bases = 3,007,133,551 bp number of sequenced bases = 3,006,459,323 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,469,408 duplication rate = 4.29% >>>>>>> Insert size mean insert size = 60,825.3375 std insert size = 2,370,083.779 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 53.9396 >>>>>>> ACTG content number of A's = 893,006,383 bp (29.7%) number of C's = 605,250,295 bp (20.13%) number of T's = 886,527,630 bp (29.49%) number of G's = 616,512,331 bp (20.51%) number of N's = 5,162,684 bp (0.17%) GC percentage = 40.64% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 26,433,442 number of insertions = 724,182 mapped reads with insertion percentage = 2.35% number of deletions = 297,701 mapped reads with deletion percentage = 0.96% homopolymer indels = 35.09% >>>>>>> Coverage mean coverageData = 0.9714X std coverageData = 2.9968X There is a 29.84% of reference with a coverageData >= 1X There is a 17.17% of reference with a coverageData >= 2X There is a 11.03% of reference with a coverageData >= 3X There is a 7.66% of reference with a coverageData >= 4X There is a 5.58% of reference with a coverageData >= 5X There is a 4.21% of reference with a coverageData >= 6X There is a 3.27% of reference with a coverageData >= 7X There is a 2.59% of reference with a coverageData >= 8X There is a 2.09% of reference with a coverageData >= 9X There is a 1.71% of reference with a coverageData >= 10X There is a 1.42% of reference with a coverageData >= 11X There is a 1.19% of reference with a coverageData >= 12X There is a 1.01% of reference with a coverageData >= 13X There is a 0.86% of reference with a coverageData >= 14X There is a 0.74% of reference with a coverageData >= 15X There is a 0.64% of reference with a coverageData >= 16X There is a 0.56% of reference with a coverageData >= 17X There is a 0.49% of reference with a coverageData >= 18X There is a 0.43% of reference with a coverageData >= 19X There is a 0.38% of reference with a coverageData >= 20X There is a 0.34% of reference with a coverageData >= 21X There is a 0.31% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.14% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.08% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 193794832 0.7775099264446768 2.809361902543974 chr2 243199373 299802410 1.23274335086382 3.1948848583724345 chr3 198022430 253080503 1.2780395786477319 3.498180149319872 chr4 191154276 143160360 0.7489257525162555 2.3040985128532574 chr5 180915260 191697941 1.0596007268817456 2.9005536712139355 chr6 171115067 137401161 0.8029752342030757 2.6519117990406222 chr7 159138663 224594982 1.4113162556857726 3.296824248961887 chr8 146364022 132973526 0.9085123801804244 3.3305474249546405 chr9 141213431 120081594 0.8503553319938809 2.658270323504977 chr10 135534747 96600168 0.7127335988608147 2.4730782919711114 chr11 135006516 223314229 1.6540996361983002 3.9160031443029313 chr12 133851895 143495895 1.0720497830830114 2.8614230714740523 chr13 115169878 129777710 1.1268372620834068 2.804930206710448 chr14 107349540 87442461 0.8145583204175817 2.972254416284235 chr15 102531392 69360500 0.6764806236123274 2.4368237921369067 chr16 90354753 76707026 0.8489539670370191 3.4308442072249923 chr17 81195210 93758214 1.1547259253347582 3.832449653625891 chr18 78077248 43025913 0.5510685135828558 2.052752291161687 chr19 59128983 43738198 0.7397082747051476 2.417220834492602 chr20 63025520 103685152 1.6451296554157744 4.916950482261631 chr21 48129895 41076429 0.8534493790190067 2.554912605046088 chr22 51304566 24828501 0.4839433004851849 2.1768096478754555 chrMT 16571 194561 11.741053647939172 5.694989346472863 chrX 155270560 131135726 0.844562716847289 2.5943864711306572 chrY 59373566 2405559 0.04051565641181128 0.6166388724060445