BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617408.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 = 30,298,478 (94.68%) number of supplementary alignments = 464,003 (1.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,232,269 number of mapped paired reads (second in pair) = 15,066,209 number of mapped paired reads (both in pair) = 29,845,546 number of mapped paired reads (singletons) = 452,932 number of mapped bases = 2,985,976,429 bp number of sequenced bases = 2,985,317,871 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,403,606 duplication rate = 4.21% >>>>>>> Insert size mean insert size = 48,089.3779 std insert size = 2,072,468.8951 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 53.9621 >>>>>>> ACTG content number of A's = 888,637,808 bp (29.77%) number of C's = 600,633,958 bp (20.12%) number of T's = 880,169,699 bp (29.48%) number of G's = 613,220,756 bp (20.54%) number of N's = 2,655,650 bp (0.09%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 29,170,200 number of insertions = 243,446 mapped reads with insertion percentage = 0.79% number of deletions = 291,457 mapped reads with deletion percentage = 0.94% homopolymer indels = 44.76% >>>>>>> Coverage mean coverageData = 0.9646X std coverageData = 2.9543X There is a 29.78% of reference with a coverageData >= 1X There is a 17.1% of reference with a coverageData >= 2X There is a 10.98% of reference with a coverageData >= 3X There is a 7.61% of reference with a coverageData >= 4X There is a 5.53% of reference with a coverageData >= 5X There is a 4.17% of reference with a coverageData >= 6X There is a 3.23% of reference with a coverageData >= 7X There is a 2.56% of reference with a coverageData >= 8X There is a 2.06% of reference with a coverageData >= 9X There is a 1.69% of reference with a coverageData >= 10X There is a 1.4% of reference with a coverageData >= 11X There is a 1.17% of reference with a coverageData >= 12X There is a 0.99% of reference with a coverageData >= 13X There is a 0.85% of reference with a coverageData >= 14X There is a 0.73% of reference with a coverageData >= 15X There is a 0.63% of reference with a coverageData >= 16X There is a 0.55% of reference with a coverageData >= 17X There is a 0.48% 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 0.33% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.19% 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 0.13% 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 0.09% 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 0.07% 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 0.05% 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 0.04% 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 0.03% 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 192331548 0.7716391928267252 2.7903753304022914 chr2 243199373 297350406 1.2226610715809698 3.0894470495996105 chr3 198022430 251783346 1.2714890227334348 3.4654295745435655 chr4 191154276 143053162 0.7483649594111094 2.291047845529372 chr5 180915260 190854112 1.0549365045270367 2.9036007708440055 chr6 171115067 136816005 0.7995555704045629 2.6183640618423367 chr7 159138663 223403494 1.403829149928198 3.248141685523833 chr8 146364022 132332457 0.9041324171865133 3.285820011984296 chr9 141213431 119426826 0.8457186059022955 2.6303173330223597 chr10 135534747 95893741 0.7075214520450612 2.436341335578591 chr11 135006516 221957444 1.6440498620081418 3.8743205433836128 chr12 133851895 142165641 1.062111530060893 2.8024949757605655 chr13 115169878 129011566 1.1201849671144046 2.7838512893263645 chr14 107349540 86631919 0.8070078269548244 2.929264954772267 chr15 102531392 68614623 0.6692060027820552 2.374319445046035 chr16 90354753 75611298 0.8368270122989545 3.3762634795589115 chr17 81195210 92454398 1.1386681307924444 3.71421465892351 chr18 78077248 42630799 0.546007961243716 2.014176160965358 chr19 59128983 42804224 0.7239127383604754 2.3585963824907186 chr20 63025520 102525611 1.6267316953513433 4.84250726542429 chr21 48129895 40920030 0.8501998601908439 2.5652693769084687 chr22 51304566 24230138 0.47228034245528944 2.114478952805489 chrMT 16571 175597 10.596644740812263 4.601438597275819 chrX 155270560 130639777 0.8413686213278293 2.5777974886546295 chrY 59373566 2358267 0.03971914033258504 0.5727606449919522