BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504625.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 = 302,017,412 number of mapped reads = 282,748,596 (93.62%) number of supplementary alignments = 2,843,462 (0.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 142,684,309 number of mapped paired reads (second in pair) = 140,064,287 number of mapped paired reads (both in pair) = 276,304,750 number of mapped paired reads (singletons) = 6,443,846 number of mapped bases = 27,062,330,510 bp number of sequenced bases = 27,036,746,169 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,383,701 duplication rate = 16.1% >>>>>>> Insert size mean insert size = 115,448.6543 std insert size = 3,180,246.0962 median insert size = 367 >>>>>>> Mapping quality mean mapping quality = 52.0881 >>>>>>> ACTG content number of A's = 7,246,790,705 bp (26.8%) number of C's = 6,213,311,080 bp (22.98%) number of T's = 7,298,800,691 bp (27%) number of G's = 6,274,170,232 bp (23.21%) number of N's = 3,673,461 bp (0.01%) GC percentage = 46.19% >>>>>>> Mismatches and indels general error rate = 0.0132 number of mismatches = 325,776,922 number of insertions = 7,943,983 mapped reads with insertion percentage = 2.6% number of deletions = 7,682,402 mapped reads with deletion percentage = 2.53% homopolymer indels = 33.67% >>>>>>> Coverage mean coverageData = 8.7419X std coverageData = 205.1012X There is a 82.22% of reference with a coverageData >= 1X There is a 72.97% of reference with a coverageData >= 2X There is a 64.31% of reference with a coverageData >= 3X There is a 56.74% of reference with a coverageData >= 4X There is a 50.13% of reference with a coverageData >= 5X There is a 44.38% of reference with a coverageData >= 6X There is a 39.36% of reference with a coverageData >= 7X There is a 34.96% of reference with a coverageData >= 8X There is a 31.1% of reference with a coverageData >= 9X There is a 27.69% of reference with a coverageData >= 10X There is a 24.68% of reference with a coverageData >= 11X There is a 22.02% of reference with a coverageData >= 12X There is a 19.65% of reference with a coverageData >= 13X There is a 17.56% of reference with a coverageData >= 14X There is a 15.7% of reference with a coverageData >= 15X There is a 14.04% of reference with a coverageData >= 16X There is a 12.57% of reference with a coverageData >= 17X There is a 11.27% of reference with a coverageData >= 18X There is a 10.11% of reference with a coverageData >= 19X There is a 9.07% of reference with a coverageData >= 20X There is a 8.15% of reference with a coverageData >= 21X There is a 7.34% of reference with a coverageData >= 22X There is a 6.61% of reference with a coverageData >= 23X There is a 5.96% of reference with a coverageData >= 24X There is a 5.38% of reference with a coverageData >= 25X There is a 4.87% of reference with a coverageData >= 26X There is a 4.41% of reference with a coverageData >= 27X There is a 4% of reference with a coverageData >= 28X There is a 3.63% of reference with a coverageData >= 29X There is a 3.3% of reference with a coverageData >= 30X There is a 3.01% of reference with a coverageData >= 31X There is a 2.75% of reference with a coverageData >= 32X There is a 2.52% of reference with a coverageData >= 33X There is a 2.31% of reference with a coverageData >= 34X There is a 2.12% of reference with a coverageData >= 35X There is a 1.95% of reference with a coverageData >= 36X There is a 1.8% of reference with a coverageData >= 37X There is a 1.66% of reference with a coverageData >= 38X There is a 1.54% of reference with a coverageData >= 39X There is a 1.43% of reference with a coverageData >= 40X There is a 1.33% of reference with a coverageData >= 41X There is a 1.24% of reference with a coverageData >= 42X There is a 1.16% of reference with a coverageData >= 43X There is a 1.09% of reference with a coverageData >= 44X There is a 1.02% of reference with a coverageData >= 45X There is a 0.96% of reference with a coverageData >= 46X There is a 0.91% of reference with a coverageData >= 47X There is a 0.86% of reference with a coverageData >= 48X There is a 0.81% of reference with a coverageData >= 49X There is a 0.77% of reference with a coverageData >= 50X There is a 0.73% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1906312754 7.648176547572172 60.12234642166645 chr2 243199373 2062639168 8.481268444717577 238.02957715628412 chr3 198022430 1367889474 6.907750167493652 22.94000136630333 chr4 191154276 1944949726 10.174764419081058 527.4396197147539 chr5 180915260 1651375780 9.127896563286038 33.79301016239814 chr6 171115067 790543465 4.619952403139345 26.194798576470575 chr7 159138663 1267680150 7.965884129615944 34.13043065535928 chr8 146364022 1489205903 10.174671908100475 138.33520308974704 chr9 141213431 706147992 5.000572445548753 74.87799704442084 chr10 135534747 2018361000 14.89183434267229 470.6122349095115 chr11 135006516 1098014396 8.133047415281792 25.218416234937596 chr12 133851895 1018066096 7.605914701469112 19.982796852416797 chr13 115169878 410035276 3.56026491579682 11.498460024110605 chr14 107349540 693347000 6.458779422808892 30.020095312803413 chr15 102531392 926777763 9.03896596858843 16.807591231760934 chr16 90354753 1453267606 16.08401946491957 201.05392977078444 chr17 81195210 887668410 10.932521881524785 72.22478841491578 chr18 78077248 458217617 5.868772641679174 278.99670022091124 chr19 59128983 1074587233 18.173612642720407 40.82083078334408 chr20 63025520 801417338 12.715759235306587 128.8552338750343 chr21 48129895 517726309 10.756855152083752 167.84389910927328 chr22 51304566 486260976 9.477927870981308 30.19500831131021 chrMT 16571 9366355 565.2256954921248 252.03258858245792 chrX 155270560 1538618630 9.909274688002672 21.33953500139856 chrY 59373566 483854093 8.149318385222138 503.5814096908411