BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926911.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 24,944,740 number of mapped reads = 23,137,674 (92.76%) number of supplementary alignments = 182,210 (0.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,638,272 number of mapped paired reads (second in pair) = 11,499,402 number of mapped paired reads (both in pair) = 22,862,718 number of mapped paired reads (singletons) = 274,956 number of mapped bases = 2,204,229,224 bp number of sequenced bases = 2,202,525,977 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,306,508 duplication rate = 4.68% >>>>>>> Insert size mean insert size = 86,391.2597 std insert size = 2,900,753.3547 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 53.4875 >>>>>>> ACTG content number of A's = 629,189,571 bp (28.57%) number of C's = 446,796,448 bp (20.29%) number of T's = 632,985,753 bp (28.74%) number of G's = 493,335,280 bp (22.4%) number of N's = 218,925 bp (0.01%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 22,471,588 number of insertions = 346,271 mapped reads with insertion percentage = 1.48% number of deletions = 1,215,525 mapped reads with deletion percentage = 5.11% homopolymer indels = 53.29% >>>>>>> Coverage mean coverageData = 0.712X std coverageData = 2.3743X There is a 28.29% of reference with a coverageData >= 1X There is a 15.62% of reference with a coverageData >= 2X There is a 9.1% of reference with a coverageData >= 3X There is a 5.68% of reference with a coverageData >= 4X There is a 3.66% of reference with a coverageData >= 5X There is a 2.43% of reference with a coverageData >= 6X There is a 1.65% of reference with a coverageData >= 7X There is a 1.14% of reference with a coverageData >= 8X There is a 0.79% of reference with a coverageData >= 9X There is a 0.56% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 184817382 0.741492162621332 2.5176255442995985 chr2 243199373 161369682 0.6635283636195888 3.2724414784346814 chr3 198022430 146982911 0.7422538497280333 1.6722817384842241 chr4 191154276 128020116 0.6697214348477353 1.646985775147876 chr5 180915260 128564797 0.7106354488836376 1.6139137143842845 chr6 171115067 131095215 0.7661231550112416 2.1643533582811147 chr7 159138663 127103960 0.7986994335876757 1.8605867610850613 chr8 146364022 117458625 0.8025102302804988 1.953681646013069 chr9 141213431 99436693 0.7041588912318121 2.7797680819954658 chr10 135534747 108125709 0.7977711353974786 5.168945220940155 chr11 135006516 116383102 0.8620554433091214 2.1873287158823476 chr12 133851895 103837514 0.7757642430090362 1.7688282312044834 chr13 115169878 69734896 0.6054959613658704 1.4979702483381563 chr14 107349540 75396507 0.7023458787061407 1.682565032280498 chr15 102531392 66516524 0.6487430113111115 1.651311531739442 chr16 90354753 70133086 0.7761969754928111 3.4035271737159696 chr17 81195210 58872787 0.7250770950650907 1.884688848415106 chr18 78077248 51888179 0.6645748963897908 2.5423843100905854 chr19 59128983 37920368 0.6413160869010719 1.9103407894423317 chr20 63025520 55236447 0.8764139827803087 1.9838542961045766 chr21 48129895 26017791 0.5405744392336613 1.9314037581959673 chr22 51304566 29955840 0.5838825339639361 1.6488824461401597 chrMT 16571 19842 1.1973930360267937 1.4275007879236283 chrX 155270560 106706605 0.6872301162564236 1.7074913929762483 chrY 59373566 2634646 0.04437405696669794 1.1365403639651364