BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013341.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,677,191 number of mapped reads = 1,486,779 (88.65%) number of supplementary alignments = 11,742 (0.7%) number of secondary alignments = 0 number of mapped bases = 98,373,708 bp number of sequenced bases = 98,326,886 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,342 duplication rate = 3.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0865 >>>>>>> ACTG content number of A's = 26,687,925 bp (27.14%) number of C's = 18,844,934 bp (19.17%) number of T's = 30,434,475 bp (30.95%) number of G's = 22,334,381 bp (22.71%) number of N's = 25,171 bp (0.03%) GC percentage = 41.88% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 790,869 number of insertions = 6,592 mapped reads with insertion percentage = 0.44% number of deletions = 26,891 mapped reads with deletion percentage = 1.79% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 0.0318X std coverageData = 0.2852X There is a 2.59% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 7282305 0.029216797818931012 0.4095353401738348 chr2 243199373 9922425 0.04079955008765586 0.34532268268593347 chr3 198022430 6110225 0.0308562267415868 0.20789410950758752 chr4 191154276 6043558 0.031616127697818276 0.2152001106191879 chr5 180915260 5204292 0.02876646226526165 0.20322812666080375 chr6 171115067 5314649 0.031058918967083127 0.24706452833538312 chr7 159138663 5990391 0.03764258720710755 0.41765541057393407 chr8 146364022 5307535 0.03626256594670513 0.2748938274060811 chr9 141213431 3643061 0.02579826135659858 0.2632600917623351 chr10 135534747 4665238 0.034420973980937894 0.304465761255364 chr11 135006516 4209628 0.031180924630334138 0.24895138177932916 chr12 133851895 4797145 0.035839201230584 0.22648283007737277 chr13 115169878 2561219 0.022238618677706684 0.17918769437755044 chr14 107349540 3227040 0.030061051030120856 0.21733227330789853 chr15 102531392 2847891 0.027775795728980254 0.19673561912618728 chr16 90354753 3428295 0.03794260828757951 0.25722650854877477 chr17 81195210 2668221 0.032861803054638324 0.23165081519873934 chr18 78077248 2451383 0.03139689298475274 0.463714888555011 chr19 59128983 2031018 0.03434894187170444 0.35111416820456176 chr20 63025520 2287748 0.03629875644024833 0.23031117511413204 chr21 48129895 1644921 0.03417670036471095 0.22996375998389812 chr22 51304566 1036583 0.020204497977821312 0.1678623955040895 chrMT 16571 261147 15.759278257196307 9.717009857050476 chrX 155270560 5224159 0.03364552172672012 0.2333825978058689 chrY 59373566 213631 0.003598082688851803 0.09106646931869322