BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006081.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 7,796,622 number of mapped reads = 6,877,961 (88.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,477,100 number of mapped paired reads (second in pair) = 3,400,861 number of mapped paired reads (both in pair) = 6,299,624 number of mapped paired reads (singletons) = 578,337 number of mapped bases = 265,394,479 bp number of sequenced bases = 265,366,544 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 435,288 duplication rate = 5.71% >>>>>>> Insert size mean insert size = 67,421.5139 std insert size = 2,524,137.6654 median insert size = 107 >>>>>>> Mapping quality mean mapping quality = 46.8999 >>>>>>> ACTG content number of A's = 70,340,142 bp (26.51%) number of C's = 59,138,496 bp (22.29%) number of T's = 72,949,534 bp (27.49%) number of G's = 62,926,984 bp (23.71%) number of N's = 11,388 bp (0%) GC percentage = 46% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,359,478 number of insertions = 8,794 mapped reads with insertion percentage = 0.13% number of deletions = 22,093 mapped reads with deletion percentage = 0.32% homopolymer indels = 44.88% >>>>>>> Coverage mean coverageData = 0.0857X std coverageData = 0.5X There is a 5.19% of reference with a coverageData >= 1X There is a 1.99% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 22777851 0.09138533299782631 0.5324189443045949 chr2 243199373 23242908 0.09557141415821002 0.5359272288798147 chr3 198022430 18199831 0.09190792679394956 0.45478933840399666 chr4 191154276 16115041 0.08430384785114615 0.44907037475788425 chr5 180915260 15769010 0.08716240962757923 0.44321273618910323 chr6 171115067 15474903 0.09043565403857745 0.499935676695524 chr7 159138663 14170358 0.08904409357768703 0.6167650245319255 chr8 146364022 13282334 0.09074862673560583 0.5317254216165814 chr9 141213431 11283744 0.07990560048073614 0.4574244274916665 chr10 135534747 12724088 0.09388063416682366 0.47496320888572024 chr11 135006516 12532058 0.09282557887798541 0.7562875756753176 chr12 133851895 12359821 0.09233952944782739 0.45983105182729445 chr13 115169878 7676348 0.06665239325859146 0.3882933212365278 chr14 107349540 8181093 0.07620985613911341 0.4232849370113054 chr15 102531392 8206586 0.08003974041433086 0.43395540654379294 chr16 90354753 8907054 0.09857869900878374 0.5175324461855959 chr17 81195210 8345827 0.10278718412083669 0.5293042762135968 chr18 78077248 6952223 0.08904287968756276 0.5519776883271639 chr19 59128983 6031856 0.10201183402731619 0.6077261431008992 chr20 63025520 6459652 0.10249264107618627 0.49556032481503914 chr21 48129895 3424358 0.07114825411524375 0.4408524221585727 chr22 51304566 3789571 0.0738642053808622 0.4561968848033584 chrMT 16571 25797 1.5567557781666768 2.4593209864265684 chrX 155270560 7780676 0.05011043948060727 0.3474840739267266 chrY 59373566 1681491 0.02832053240662688 0.27357888705904493