BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549154.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 15,894,191 number of mapped reads = 13,544,458 (85.22%) number of secondary alignments = 0 number of mapped bases = 537,450,867 bp number of sequenced bases = 537,396,623 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 944,228 duplication rate = 5.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9012 >>>>>>> ACTG content number of A's = 158,259,848 bp (29.45%) number of C's = 108,684,831 bp (20.22%) number of T's = 160,633,894 bp (29.89%) number of G's = 109,704,501 bp (20.41%) number of N's = 113,549 bp (0.02%) GC percentage = 40.64% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,700,007 number of insertions = 13,651 mapped reads with insertion percentage = 0.1% number of deletions = 42,644 mapped reads with deletion percentage = 0.31% homopolymer indels = 44.09% >>>>>>> Coverage mean coverageData = 0.1736X std coverageData = 1.6486X There is a 11.03% of reference with a coverageData >= 1X There is a 3.79% of reference with a coverageData >= 2X There is a 1.37% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 43506721 0.17455010071970894 1.9875050336395443 chr2 243199373 46534657 0.1913436553144403 0.9031368346979205 chr3 198022430 37312062 0.18842341243868183 0.6203330894814864 chr4 191154276 37001286 0.19356766050056867 0.7221334454066328 chr5 180915260 34499261 0.19069292993858009 0.6376236855962768 chr6 171115067 32441655 0.18958970456996635 0.6937735240951718 chr7 159138663 30073746 0.18897824974186192 1.3221454268340407 chr8 146364022 28795791 0.19674091082301634 6.155279300086286 chr9 141213431 22956288 0.16256448014495165 0.836237503312921 chr10 135534747 25094033 0.18514833690581206 0.9721191082595396 chr11 135006516 25085415 0.18580892051165887 0.806108457317269 chr12 133851895 24893708 0.18597949621856305 0.6487913333135547 chr13 115169878 17853522 0.1550190232901002 0.55726793168586 chr14 107349540 16809995 0.1565912159474554 0.7462546790008352 chr15 102531392 15592763 0.15207794116361942 0.5543738652790527 chr16 90354753 14487740 0.16034286541627754 0.6337784340154997 chr17 81195210 13602970 0.16753414394765406 0.6472379926278393 chr18 78077248 14543103 0.1862655686839782 1.6253054372569185 chr19 59128983 9477696 0.1602885001421384 1.5456442856128292 chr20 63025520 11023455 0.17490462593565273 0.660856554237847 chr21 48129895 7138189 0.14831091985552847 0.6881640874928427 chr22 51304566 5765571 0.11237929583109621 0.5235544780894321 chrMT 16571 15110 0.9118339267394846 1.5359665134981153 chrX 155270560 18168907 0.1170145003663283 0.6075597953727195 chrY 59373566 4777223 0.0804604358781482 0.7797649477689533