BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818972.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,271,896 number of mapped reads = 2,241,508 (98.66%) number of supplementary alignments = 36,646 (1.61%) number of secondary alignments = 0 number of mapped bases = 207,399,494 bp number of sequenced bases = 207,273,487 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,115,483 duplication rate = 42.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0981 >>>>>>> ACTG content number of A's = 60,429,006 bp (29.15%) number of C's = 43,730,029 bp (21.1%) number of T's = 57,519,217 bp (27.75%) number of G's = 45,585,253 bp (21.99%) number of N's = 9,982 bp (0%) GC percentage = 43.09% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,285,500 number of insertions = 35,920 mapped reads with insertion percentage = 1.56% number of deletions = 67,667 mapped reads with deletion percentage = 2.95% homopolymer indels = 39.72% >>>>>>> Coverage mean coverageData = 0.067X std coverageData = 0.7804X There is a 2.78% of reference with a coverageData >= 1X There is a 1.48% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% 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 21040501 0.08441503943133606 1.357282871052317 chr2 243199373 16607244 0.06828654118281793 1.1040284061449925 chr3 198022430 12103639 0.06112256576186849 0.4850948936991203 chr4 191154276 11565289 0.06050238185621336 0.5434480358006823 chr5 180915260 11030565 0.06097089322371148 0.5006153859768936 chr6 171115067 8696295 0.05082132831704411 0.5259437536326411 chr7 159138663 10111002 0.06353579833707663 0.8970706991330872 chr8 146364022 19254627 0.13155300556034188 0.800818152345552 chr9 141213431 8979442 0.06358773337927041 0.7229581495328172 chr10 135534747 10763564 0.07941553172338899 0.9100822913791923 chr11 135006516 7061524 0.0523050605942605 0.524430863951865 chr12 133851895 9308670 0.0695445514611504 0.533787408900822 chr13 115169878 4382239 0.03805021830447715 0.3800663453802164 chr14 107349540 4803208 0.0447436290830869 0.4406793234550355 chr15 102531392 5485626 0.05350191675930821 0.46812310121833145 chr16 90354753 6389087 0.07071113348071462 0.9035139228730069 chr17 81195210 7068773 0.08705899030250676 0.651833233623679 chr18 78077248 4934754 0.06320348278668839 0.8373210168456245 chr19 59128983 4167651 0.0704840636274769 1.2275686057303326 chr20 63025520 5947776 0.09437091514675325 0.6552705080944675 chr21 48129895 2784720 0.057858426659771436 0.512148164996882 chr22 51304566 1656919 0.032295741474550235 0.39060549767062314 chrMT 16571 22561 1.361474865729286 2.024471537719451 chrX 155270560 12502289 0.08051937856088108 0.6166599234532237 chrY 59373566 731529 0.012320785987488102 0.7206930449590531