BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163508.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 205,534,476 number of mapped reads = 198,826,736 (96.74%) number of supplementary alignments = 81,128 (0.04%) number of secondary alignments = 0 number of mapped bases = 19,781,993,561 bp number of sequenced bases = 19,779,074,921 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,502,557 duplication rate = 52.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.8609 >>>>>>> ACTG content number of A's = 4,874,066,234 bp (24.64%) number of C's = 5,011,681,167 bp (25.34%) number of T's = 4,960,913,575 bp (25.08%) number of G's = 4,927,335,230 bp (24.91%) number of N's = 5,078,715 bp (0.03%) GC percentage = 50.25% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 125,299,537 number of insertions = 948,910 mapped reads with insertion percentage = 0.47% number of deletions = 1,306,565 mapped reads with deletion percentage = 0.65% homopolymer indels = 44.56% >>>>>>> Coverage mean coverageData = 6.3902X std coverageData = 56.9903X There is a 13.53% of reference with a coverageData >= 1X There is a 8.46% of reference with a coverageData >= 2X There is a 6.89% of reference with a coverageData >= 3X There is a 6.28% of reference with a coverageData >= 4X There is a 5.88% of reference with a coverageData >= 5X There is a 5.6% of reference with a coverageData >= 6X There is a 5.39% of reference with a coverageData >= 7X There is a 5.21% of reference with a coverageData >= 8X There is a 5.06% of reference with a coverageData >= 9X There is a 4.94% of reference with a coverageData >= 10X There is a 4.83% of reference with a coverageData >= 11X There is a 4.73% of reference with a coverageData >= 12X There is a 4.64% of reference with a coverageData >= 13X There is a 4.56% of reference with a coverageData >= 14X There is a 4.49% of reference with a coverageData >= 15X There is a 4.42% of reference with a coverageData >= 16X There is a 4.36% of reference with a coverageData >= 17X There is a 4.3% of reference with a coverageData >= 18X There is a 4.25% of reference with a coverageData >= 19X There is a 4.19% of reference with a coverageData >= 20X There is a 4.15% of reference with a coverageData >= 21X There is a 4.1% of reference with a coverageData >= 22X There is a 4.05% of reference with a coverageData >= 23X There is a 4.01% of reference with a coverageData >= 24X There is a 3.97% of reference with a coverageData >= 25X There is a 3.93% of reference with a coverageData >= 26X There is a 3.89% of reference with a coverageData >= 27X There is a 3.86% of reference with a coverageData >= 28X There is a 3.82% of reference with a coverageData >= 29X There is a 3.79% of reference with a coverageData >= 30X There is a 3.75% of reference with a coverageData >= 31X There is a 3.72% of reference with a coverageData >= 32X There is a 3.69% of reference with a coverageData >= 33X There is a 3.66% of reference with a coverageData >= 34X There is a 3.63% of reference with a coverageData >= 35X There is a 3.6% of reference with a coverageData >= 36X There is a 3.57% of reference with a coverageData >= 37X There is a 3.54% of reference with a coverageData >= 38X There is a 3.51% of reference with a coverageData >= 39X There is a 3.49% of reference with a coverageData >= 40X There is a 3.46% of reference with a coverageData >= 41X There is a 3.43% of reference with a coverageData >= 42X There is a 3.41% of reference with a coverageData >= 43X There is a 3.38% of reference with a coverageData >= 44X There is a 3.36% of reference with a coverageData >= 45X There is a 3.33% of reference with a coverageData >= 46X There is a 3.31% of reference with a coverageData >= 47X There is a 3.29% of reference with a coverageData >= 48X There is a 3.26% of reference with a coverageData >= 49X There is a 3.24% of reference with a coverageData >= 50X There is a 3.22% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2002155724 8.032701045908327 52.910938579168125 chr2 243199373 1267242238 5.210713425646866 39.3745183308075 chr3 198022430 985161303 4.974998554456684 37.83966016272054 chr4 191154276 787404562 4.119209773785024 52.92653100324126 chr5 180915260 946628485 5.232441337452683 56.172624521187046 chr6 171115067 855583537 5.000047932658087 33.94665999072269 chr7 159138663 1232972234 7.747785552276508 127.78526121383106 chr8 146364022 1009562181 6.897611634367358 108.31897134229804 chr9 141213431 861401298 6.099995530878362 41.863467740372855 chr10 135534747 764800387 5.642836275778048 36.59434105574483 chr11 135006516 984328461 7.29097002251358 41.79478405547893 chr12 133851895 867555590 6.481459153043743 36.533583812519076 chr13 115169878 337312090 2.928822152611814 24.006439439634164 chr14 107349540 530093578 4.938014433969628 34.432883161252875 chr15 102531392 881455283 8.596930811199755 53.13804530698937 chr16 90354753 878204594 9.719517400484731 53.600299693823246 chr17 81195210 1091724272 13.445673359302846 67.94439042275987 chr18 78077248 297621374 3.8118835079842976 40.33938198712405 chr19 59128983 1154283384 19.521448288735154 72.6501914758342 chr20 63025520 435460467 6.909272101205987 41.2553075386528 chr21 48129895 254577447 5.289382970812631 49.184494678427505 chr22 51304566 486449840 9.481609102784342 56.24767241767644 chrMT 16571 1002811 60.51602196608533 19.860529460614018 chrX 155270560 833480509 5.367923636006723 36.87957662762575 chrY 59373566 35531912 0.5984466555369101 30.48967081438155