BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081043.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,544,416 number of mapped reads = 1,199,112 (77.64%) number of supplementary alignments = 6,521 (0.42%) number of secondary alignments = 0 number of mapped bases = 80,731,179 bp number of sequenced bases = 80,701,150 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,407 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4066 >>>>>>> ACTG content number of A's = 24,230,877 bp (30.03%) number of C's = 15,147,483 bp (18.77%) number of T's = 23,818,491 bp (29.51%) number of G's = 17,503,264 bp (21.69%) number of N's = 1,035 bp (0%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 659,365 number of insertions = 5,279 mapped reads with insertion percentage = 0.44% number of deletions = 17,167 mapped reads with deletion percentage = 1.42% homopolymer indels = 48.13% >>>>>>> Coverage mean coverageData = 0.0261X std coverageData = 0.2222X There is a 2.36% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6400378 0.025678483665643504 0.33667872498912194 chr2 243199373 7417210 0.030498475010459835 0.24023902580996134 chr3 198022430 6120001 0.030905594886397464 0.1899627469005828 chr4 191154276 4894072 0.025602733574215206 0.17614678461704913 chr5 180915260 5264727 0.02910051368801062 0.18442439914297545 chr6 171115067 4655471 0.02720666906555926 0.21730549173668723 chr7 159138663 4447522 0.02794746365312872 0.30327962844609696 chr8 146364022 3670750 0.025079592305819527 0.22640321277580366 chr9 141213431 3126275 0.022138651953014298 0.20174885978678966 chr10 135534747 3557939 0.026251120681252314 0.20305303434571134 chr11 135006516 3395532 0.025150874939991786 0.2000273719954739 chr12 133851895 3789634 0.028312143059311935 0.18308166864669304 chr13 115169878 2390420 0.020755600696216767 0.15492740621220744 chr14 107349540 2602383 0.024242143934664274 0.17414821439871386 chr15 102531392 2288239 0.02231744790902673 0.16481271114306795 chr16 90354753 2461444 0.02724199799428371 0.19024572471993337 chr17 81195210 1993674 0.024554083917019243 0.18049893544880036 chr18 78077248 2332281 0.02987145499800403 0.3688988545117615 chr19 59128983 1398188 0.02364640704204231 0.24638185840512078 chr20 63025520 1756808 0.02787454986488013 0.1828970247300019 chr21 48129895 1118052 0.023229886539332778 0.17183421799579243 chr22 51304566 836179 0.016298334927928246 0.13687772104362222 chrMT 16571 5595 0.3376380423631646 0.644110128609681 chrX 155270560 4622854 0.029772894488175994 0.1985700717087362 chrY 59373566 185551 0.0031251449508692135 0.07031967662757521