BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236100.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,609,768 number of mapped reads = 476,941 (29.63%) number of supplementary alignments = 3,143 (0.2%) number of secondary alignments = 0 number of mapped bases = 31,237,479 bp number of sequenced bases = 31,224,017 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,499 duplication rate = 4.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.182 >>>>>>> ACTG content number of A's = 8,559,059 bp (27.41%) number of C's = 5,561,684 bp (17.81%) number of T's = 10,148,049 bp (32.5%) number of G's = 6,942,552 bp (22.23%) number of N's = 12,673 bp (0.04%) GC percentage = 40.05% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 257,251 number of insertions = 2,388 mapped reads with insertion percentage = 0.5% number of deletions = 7,523 mapped reads with deletion percentage = 1.56% homopolymer indels = 48.32% >>>>>>> Coverage mean coverageData = 0.0101X std coverageData = 0.1605X There is a 0.81% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 3099224 0.012434167616376772 0.22519017187942655 chr2 243199373 2160979 0.008885627349047484 0.14464030555945373 chr3 198022430 1766922 0.008922837680559723 0.11300649658204534 chr4 191154276 1991294 0.010417208768063341 0.12914398716763995 chr5 180915260 2517637 0.013916111885752478 0.14325247476341815 chr6 171115067 2268209 0.013255460432365081 0.14709253762006083 chr7 159138663 1731910 0.010883024699032441 0.1542250896040102 chr8 146364022 2110820 0.01442171355471497 0.16831649387629233 chr9 141213431 1536367 0.010879751232727997 0.14051853046524002 chr10 135534747 1337873 0.00987107018394331 0.15057265527209962 chr11 135006516 1153237 0.008542083998375308 0.11954538182478919 chr12 133851895 1108559 0.008281982111646607 0.10933139697701806 chr13 115169878 857433 0.007444941462905778 0.1059630267277375 chr14 107349540 692983 0.006455388630449651 0.09711622691970326 chr15 102531392 726506 0.007085693326001075 0.10227943761114465 chr16 90354753 678536 0.007509687951888928 0.10555028233747457 chr17 81195210 614554 0.007568845502093042 0.10712214479623551 chr18 78077248 795822 0.010192751670755609 0.17338168245073826 chr19 59128983 392544 0.006638774761270627 0.15193848701482507 chr20 63025520 638589 0.010132228976452714 0.12130462947605869 chr21 48129895 498934 0.010366405328746301 0.1263327508419289 chr22 51304566 357786 0.006973765259021975 0.09861459710231685 chrMT 16571 472827 28.533401725906703 15.776063125701553 chrX 155270560 1639388 0.010558266808595267 0.12623699280003015 chrY 59373566 88546 0.001491337070776581 0.062408190721894366