BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094004.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 = 491,890 number of mapped reads = 413,426 (84.05%) number of supplementary alignments = 957 (0.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 207,130 number of mapped paired reads (second in pair) = 206,296 number of mapped paired reads (both in pair) = 410,548 number of mapped paired reads (singletons) = 2,878 number of mapped bases = 59,537,430 bp number of sequenced bases = 59,109,298 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 408,377 duplication rate = 46.17% >>>>>>> Insert size mean insert size = 26,463.8791 std insert size = 1,908,372.4305 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 26.2339 >>>>>>> ACTG content number of A's = 17,166,364 bp (29.04%) number of C's = 12,135,702 bp (20.53%) number of T's = 16,928,000 bp (28.64%) number of G's = 12,878,628 bp (21.79%) number of N's = 604 bp (0%) GC percentage = 42.32% >>>>>>> Mismatches and indels general error rate = 0.0238 number of mismatches = 1,398,352 number of insertions = 6,799 mapped reads with insertion percentage = 1.6% number of deletions = 82,647 mapped reads with deletion percentage = 19.55% homopolymer indels = 31.91% >>>>>>> Coverage mean coverageData = 0.0192X std coverageData = 29.9144X There is a 0% 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 944367 0.003788825063749791 3.024883030988129 chr2 243199373 971849 0.003996099940603054 2.570498154576115 chr3 198022430 521997 0.002636049865664208 1.9174103382834613 chr4 191154276 337081 0.0017633976443195024 1.2510643950564733 chr5 180915260 26156 1.4457597440923446E-4 0.053000848022518254 chr6 171115067 358075 0.002092597725482584 2.0762846689073142 chr7 159138663 116433 7.316449554436687E-4 0.35758296567444264 chr8 146364022 221583 0.0015139171291698994 1.3696522177799084 chr9 141213431 1075246 0.007614332378908066 4.412058248043431 chr10 135534747 2250432 0.016604096365045045 13.592711727858639 chr11 135006516 904226 0.006697647097270476 5.703498149829772 chr12 133851895 154587 0.0011549108064551495 0.9703443785653505 chr13 115169878 45183 3.9231612279731683E-4 0.24207582116370985 chr14 107349540 134911 0.001256745021916256 1.017013506344763 chr15 102531392 109374 0.0010667367122061504 0.4960263527912724 chr16 90354753 21073 2.3322514090653315E-4 0.06454860479816737 chr17 81195210 621762 0.007657619211773699 4.203944204051422 chr18 78077248 61873 7.924587710878335E-4 0.6196644496265815 chr19 59128983 38535 6.517108538802367E-4 0.26758248109039284 chr20 63025520 124236 0.001971201506945123 1.1417130104276887 chr21 48129895 26516 5.50925781159506E-4 0.27846629373915416 chr22 51304566 29271 5.705340144578944E-4 0.1604463132160086 chrMT 16571 36919934 2227.9846720173796 12135.83543750019 chrX 155270560 13519219 0.08706878496477374 36.561354937702006 chrY 59373566 3511 5.913405975986014E-5 0.019578438205523956