BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960904.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 = 153,141,410 number of mapped reads = 149,965,619 (97.93%) number of supplementary alignments = 310,521 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 75,217,867 number of mapped paired reads (second in pair) = 74,747,752 number of mapped paired reads (both in pair) = 148,948,574 number of mapped paired reads (singletons) = 1,017,045 number of mapped bases = 14,771,522,032 bp number of sequenced bases = 14,767,178,467 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,246,490 duplication rate = 4.83% >>>>>>> Insert size mean insert size = 20,485.7962 std insert size = 1,350,393.283 median insert size = 150 >>>>>>> Mapping quality mean mapping quality = 53.6399 >>>>>>> ACTG content number of A's = 4,367,837,746 bp (29.58%) number of C's = 3,006,076,281 bp (20.36%) number of T's = 4,359,229,885 bp (29.52%) number of G's = 3,028,169,116 bp (20.51%) number of N's = 5,865,439 bp (0.04%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 142,586,399 number of insertions = 1,649,224 mapped reads with insertion percentage = 1.07% number of deletions = 1,803,683 mapped reads with deletion percentage = 1.16% homopolymer indels = 40.92% >>>>>>> Coverage mean coverageData = 4.7716X std coverageData = 50.4522X There is a 88.73% of reference with a coverageData >= 1X There is a 82.64% of reference with a coverageData >= 2X There is a 72.74% of reference with a coverageData >= 3X There is a 60.49% of reference with a coverageData >= 4X There is a 47.37% of reference with a coverageData >= 5X There is a 35.11% of reference with a coverageData >= 6X There is a 24.68% of reference with a coverageData >= 7X There is a 16.56% of reference with a coverageData >= 8X There is a 10.66% of reference with a coverageData >= 9X There is a 6.62% of reference with a coverageData >= 10X There is a 4.01% of reference with a coverageData >= 11X There is a 2.39% of reference with a coverageData >= 12X There is a 1.43% of reference with a coverageData >= 13X There is a 0.87% of reference with a coverageData >= 14X There is a 0.55% of reference with a coverageData >= 15X There is a 0.38% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.19% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.15% of reference with a coverageData >= 21X There is a 0.13% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.11% of reference with a coverageData >= 24X There is a 0.11% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.09% of reference with a coverageData >= 27X There is a 0.09% of reference with a coverageData >= 28X There is a 0.08% of reference with a coverageData >= 29X There is a 0.08% of reference with a coverageData >= 30X There is a 0.08% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% 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 0.05% 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 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1202490003 4.824421292013551 125.35602613999386 chr2 243199373 1269334280 5.219315594205911 32.29553033870476 chr3 198022430 981671154 4.957373535917118 8.762421863048417 chr4 191154276 998026704 5.221053511771822 39.5025207903935 chr5 180915260 894076728 4.941964143875978 5.256578528468519 chr6 171115067 851324955 4.975160691138905 15.457234691396128 chr7 159138663 791212678 4.97184444737983 32.29605747163506 chr8 146364022 748278748 5.112450025457759 56.64824209856298 chr9 141213431 616399459 4.365020059600422 45.09672880547256 chr10 135534747 757772559 5.590983683320706 105.84623505205387 chr11 135006516 665907773 4.932412099279712 20.747238273643816 chr12 133851895 653065133 4.879012979233503 4.7418476018544435 chr13 115169878 473641081 4.112543047063053 3.371560886864559 chr14 107349540 436030148 4.061779379771911 4.910953912599254 chr15 102531392 408370530 3.982882920384032 3.4380223337783398 chr16 90354753 457463119 5.062966848019606 42.707996927105214 chr17 81195210 388289024 4.782166632736094 19.406166995327432 chr18 78077248 405478377 5.193297501981627 54.12116523718341 chr19 59128983 278815886 4.715384433383541 61.15896836164342 chr20 63025520 300969753 4.7753632655470355 15.723439672105785 chr21 48129895 202097886 4.199009492956509 20.80187843997227 chr22 51304566 167962283 3.2738271872331985 4.215567796845936 chrMT 16571 11403088 688.1351759097219 100.72857490575231 chrX 155270560 765030418 4.927079660175116 16.10762897762031 chrY 59373566 46410265 0.7816654468758033 43.08895698067925