BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006043.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 8,156,214 number of mapped reads = 7,109,087 (87.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,610,327 number of mapped paired reads (second in pair) = 3,498,760 number of mapped paired reads (both in pair) = 6,603,852 number of mapped paired reads (singletons) = 505,235 number of mapped bases = 275,123,214 bp number of sequenced bases = 275,093,513 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 225,523 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 48,566.9931 std insert size = 2,158,402.2173 median insert size = 93 >>>>>>> Mapping quality mean mapping quality = 47.7194 >>>>>>> ACTG content number of A's = 76,025,870 bp (27.64%) number of C's = 60,141,951 bp (21.86%) number of T's = 77,381,558 bp (28.13%) number of G's = 61,434,243 bp (22.33%) number of N's = 109,891 bp (0.04%) GC percentage = 44.19% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,540,402 number of insertions = 8,496 mapped reads with insertion percentage = 0.12% number of deletions = 23,306 mapped reads with deletion percentage = 0.33% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 0.0889X std coverageData = 0.4426X There is a 6.74% of reference with a coverageData >= 1X There is a 1.58% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 23602622 0.0946943357866298 0.5122575346821855 chr2 243199373 23988894 0.09863879871104766 0.5014804227662145 chr3 198022430 18541054 0.09363108007512078 0.3789907574458468 chr4 191154276 17662119 0.09239719544646754 0.39860674522566497 chr5 180915260 16357785 0.09041683382595808 0.37334873737080276 chr6 171115067 15967225 0.09331279401597055 0.4118017172940822 chr7 159138663 14819390 0.09312249908747819 0.6042004380593075 chr8 146364022 14535086 0.09930777933937891 0.4642061706279172 chr9 141213431 11697622 0.08283646900414168 0.4275561577663696 chr10 135534747 13462622 0.09932967226478093 0.42876434392187096 chr11 135006516 12758448 0.09450246090344262 0.5724918610677238 chr12 133851895 12919912 0.09652393789419268 0.3893660520285056 chr13 115169878 8983339 0.07800076856901768 0.348608050123831 chr14 107349540 8336481 0.0776573518619642 0.36260959275929006 chr15 102531392 8261620 0.08057649309979133 0.3529751237395131 chr16 90354753 8640967 0.09563378475507536 0.4280880986587333 chr17 81195210 7968983 0.09814597437459673 0.44199440873808704 chr18 78077248 7229803 0.09259807671499898 0.6027000987876493 chr19 59128983 5962150 0.1008329536126133 0.5124462268517128 chr20 63025520 6282368 0.09967974877478203 0.40114942035535434 chr21 48129895 3451693 0.07171619634740528 0.3949124428420629 chr22 51304566 3546077 0.06911815607211257 0.3644000809751933 chrMT 16571 15285 0.9223945446865005 1.5434856706062876 chrX 155270560 8303251 0.05347601631629331 0.311152479220891 chrY 59373566 1828418 0.030795152172601526 0.27902743337396335