BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093975.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 445,312 number of mapped reads = 365,494 (82.08%) number of supplementary alignments = 11,072 (2.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 182,853 number of mapped paired reads (second in pair) = 182,641 number of mapped paired reads (both in pair) = 362,648 number of mapped paired reads (singletons) = 2,846 number of mapped bases = 50,823,354 bp number of sequenced bases = 50,784,944 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 368,428 duplication rate = 32.69% >>>>>>> Insert size mean insert size = 87,122.5307 std insert size = 2,998,959.2129 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 17.6744 >>>>>>> ACTG content number of A's = 13,139,838 bp (25.87%) number of C's = 10,567,295 bp (20.81%) number of T's = 14,771,262 bp (29.09%) number of G's = 12,305,850 bp (24.23%) number of N's = 699 bp (0%) GC percentage = 45.04% >>>>>>> Mismatches and indels general error rate = 0.0252 number of mismatches = 1,261,503 number of insertions = 8,622 mapped reads with insertion percentage = 1.97% number of deletions = 16,022 mapped reads with deletion percentage = 4.29% homopolymer indels = 39.22% >>>>>>> Coverage mean coverageData = 0.0164X std coverageData = 43.6363X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% 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 463813 0.0018608298673005112 1.9325475457649681 chr2 243199373 901497 0.003706822879021156 2.4162662136321504 chr3 198022430 577568 0.002916679691285477 2.1805276532217315 chr4 191154276 31452 1.6453725576089128E-4 0.032457408614520844 chr5 180915260 1267613 0.00700666709928173 5.9467949248302805 chr6 171115067 128659 7.51885864030898E-4 0.6147006664606717 chr7 159138663 580466 0.0036475485533015947 2.407084130246913 chr8 146364022 88465 6.044176621492405E-4 0.30904098638744176 chr9 141213431 370031 0.002620366896970303 1.8085744853324743 chr10 135534747 90880 6.705291595814909E-4 0.37199639704090537 chr11 135006516 109877 8.138644211809747E-4 0.4368812572302658 chr12 133851895 41567 3.105447255714983E-4 0.09412032337478081 chr13 115169878 184787 0.001604473350227913 1.3285995402170294 chr14 107349540 49012 4.565646019535808E-4 0.20172207875588127 chr15 102531392 18796 1.8331946571056013E-4 0.0472535933298574 chr16 90354753 83451 9.235928075637592E-4 0.30776004540297874 chr17 81195210 1865314 0.022973202483249935 12.115596750696465 chr18 78077248 2553855 0.032709336784001404 17.08922777110771 chr19 59128983 20360 3.44331983521516E-4 0.10836148335595026 chr20 63025520 827763 0.013133775016850317 7.829776141977898 chr21 48129895 8975 1.8647453936893068E-4 0.04054108938261779 chr22 51304566 20558 4.0070507564570374E-4 0.09288157085838385 chrMT 16571 34909397 2106.6560255868685 18525.473016893007 chrX 155270560 5624278 0.03622243650051884 23.261844007596896 chrY 59373566 4920 8.286515921917172E-5 0.028099590622990157