BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16352033.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 1,377,826,506 number of mapped reads = 1,337,738,496 (97.09%) number of supplementary alignments = 29,654,945 (2.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 669,606,424 number of mapped paired reads (second in pair) = 668,132,072 number of mapped paired reads (both in pair) = 1,326,143,868 number of mapped paired reads (singletons) = 11,594,628 number of mapped bases = 120,920,032,356 bp number of sequenced bases = 120,840,542,924 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 470,335,212 duplication rate = 31.28% >>>>>>> Insert size mean insert size = 130,699.0478 std insert size = 3,511,771.7532 median insert size = 282 >>>>>>> Mapping quality mean mapping quality = 52.9314 >>>>>>> ACTG content number of A's = 35,056,797,032 bp (29.01%) number of C's = 25,136,543,834 bp (20.8%) number of T's = 34,778,073,552 bp (28.78%) number of G's = 25,866,593,298 bp (21.41%) number of N's = 2,535,208 bp (0%) GC percentage = 42.21% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 903,156,853 number of insertions = 16,152,958 mapped reads with insertion percentage = 1.18% number of deletions = 53,259,770 mapped reads with deletion percentage = 3.9% homopolymer indels = 45.5% >>>>>>> Coverage mean coverageData = 39.0607X std coverageData = 370.3229X There is a 91.8% of reference with a coverageData >= 1X There is a 91.73% of reference with a coverageData >= 2X There is a 91.69% of reference with a coverageData >= 3X There is a 91.65% of reference with a coverageData >= 4X There is a 91.63% of reference with a coverageData >= 5X There is a 91.6% of reference with a coverageData >= 6X There is a 91.57% of reference with a coverageData >= 7X There is a 91.54% of reference with a coverageData >= 8X There is a 91.51% of reference with a coverageData >= 9X There is a 91.48% of reference with a coverageData >= 10X There is a 91.44% of reference with a coverageData >= 11X There is a 91.4% of reference with a coverageData >= 12X There is a 91.35% of reference with a coverageData >= 13X There is a 91.29% of reference with a coverageData >= 14X There is a 91.21% of reference with a coverageData >= 15X There is a 91.11% of reference with a coverageData >= 16X There is a 90.99% of reference with a coverageData >= 17X There is a 90.83% of reference with a coverageData >= 18X There is a 90.62% of reference with a coverageData >= 19X There is a 90.34% of reference with a coverageData >= 20X There is a 89.99% of reference with a coverageData >= 21X There is a 89.52% of reference with a coverageData >= 22X There is a 88.93% of reference with a coverageData >= 23X There is a 88.18% of reference with a coverageData >= 24X There is a 87.25% of reference with a coverageData >= 25X There is a 86.11% of reference with a coverageData >= 26X There is a 84.73% of reference with a coverageData >= 27X There is a 83.11% of reference with a coverageData >= 28X There is a 81.21% of reference with a coverageData >= 29X There is a 79.04% of reference with a coverageData >= 30X There is a 76.6% of reference with a coverageData >= 31X There is a 73.88% of reference with a coverageData >= 32X There is a 70.92% of reference with a coverageData >= 33X There is a 67.74% of reference with a coverageData >= 34X There is a 64.36% of reference with a coverageData >= 35X There is a 60.82% of reference with a coverageData >= 36X There is a 57.17% of reference with a coverageData >= 37X There is a 53.45% of reference with a coverageData >= 38X There is a 49.69% of reference with a coverageData >= 39X There is a 45.96% of reference with a coverageData >= 40X There is a 42.28% of reference with a coverageData >= 41X There is a 38.69% of reference with a coverageData >= 42X There is a 35.23% of reference with a coverageData >= 43X There is a 31.92% of reference with a coverageData >= 44X There is a 28.78% of reference with a coverageData >= 45X There is a 25.84% of reference with a coverageData >= 46X There is a 23.1% of reference with a coverageData >= 47X There is a 20.57% of reference with a coverageData >= 48X There is a 18.25% of reference with a coverageData >= 49X There is a 16.13% of reference with a coverageData >= 50X There is a 14.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9786452723 39.26350387307561 844.843203898967 chr2 243199373 10209775340 41.98109236079322 361.9948249028916 chr3 198022430 7886643638 39.82702180758008 36.35930073988945 chr4 191154276 7900012729 41.327941463365434 260.4401471107219 chr5 180915260 7185551145 39.71777253615864 27.749534580199708 chr6 171115067 6801948038 39.750725387613 100.29751230160332 chr7 159138663 6473034603 40.67543663477932 253.30975531647746 chr8 146364022 6113215549 41.76720115685261 561.4899556403582 chr9 141213431 5121628328 36.26870540380823 259.09839584317484 chr10 135534747 6278392480 46.32312096321691 780.5242289805504 chr11 135006516 5417912734 40.13074994098803 128.9387856251529 chr12 133851895 5306881861 39.647416728765776 38.806503640871014 chr13 115169878 3814545916 33.121038089490725 22.58517937285286 chr14 107349540 3594704313 33.48597779738972 36.01156956025489 chr15 102531392 3399451648 33.15522769845941 24.43518089260562 chr16 90354753 3936994368 43.57263162459201 318.6051353280041 chr17 81195210 3378584026 41.61063227744592 148.54131037376555 chr18 78077248 3274385510 41.9377679653873 465.2093448055204 chr19 59128983 2538072408 42.924337257753955 353.2648505983453 chr20 63025520 2513899402 39.8870077073541 48.07204596424494 chr21 48129895 1657427827 34.43655605315573 88.56380576841923 chr22 51304566 1495331842 29.146174669911446 34.36246188505831 chrMT 16571 357050255 21546.69331965482 3640.949403287225 chrX 155270560 6066862496 39.07284482003543 75.81643811085847 chrY 59373566 411273177 6.926873433877965 255.51272589881174