BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926949.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 13,783,760 number of mapped reads = 13,565,659 (98.42%) number of supplementary alignments = 279,023 (2.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,781,952 number of mapped paired reads (second in pair) = 6,783,707 number of mapped paired reads (both in pair) = 13,428,780 number of mapped paired reads (singletons) = 136,879 number of mapped bases = 1,251,558,552 bp number of sequenced bases = 1,250,633,847 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 799,321 duplication rate = 4.72% >>>>>>> Insert size mean insert size = 202,929.3458 std insert size = 4,400,697.5156 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.2241 >>>>>>> ACTG content number of A's = 357,564,974 bp (28.59%) number of C's = 246,022,622 bp (19.67%) number of T's = 364,506,399 bp (29.15%) number of G's = 282,485,579 bp (22.59%) number of N's = 54,273 bp (0%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 11,438,158 number of insertions = 204,714 mapped reads with insertion percentage = 1.48% number of deletions = 645,494 mapped reads with deletion percentage = 4.64% homopolymer indels = 52.52% >>>>>>> Coverage mean coverageData = 0.4043X std coverageData = 1.7097X There is a 22.1% of reference with a coverageData >= 1X There is a 9.43% of reference with a coverageData >= 2X There is a 4.07% of reference with a coverageData >= 3X There is a 1.95% of reference with a coverageData >= 4X There is a 0.98% of reference with a coverageData >= 5X There is a 0.52% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 103309436 0.41448015489598317 2.149794741362174 chr2 243199373 109095266 0.44858366472844485 3.0005302394441697 chr3 198022430 83923152 0.42380629305478174 1.0039279822745522 chr4 191154276 75097641 0.39286403930613617 1.2825507467187693 chr5 180915260 76494190 0.4228177877311179 0.9870924996103128 chr6 171115067 73422691 0.42908372878701556 1.1929301332663844 chr7 159138663 65970118 0.4145448802721184 1.2471402130803737 chr8 146364022 62590885 0.4276384602221439 1.1174931262007146 chr9 141213431 52624961 0.3726625762672674 1.9229069922060458 chr10 135534747 61188123 0.4514570938771886 3.1689976953359924 chr11 135006516 60751363 0.44998837685730664 1.9448309644902146 chr12 133851895 57119870 0.4267393450051641 1.0469500754013736 chr13 115169878 37575770 0.3262638690995227 0.8662802443666139 chr14 107349540 38159623 0.3554707640107261 0.9361262394729207 chr15 102531392 36410718 0.35511775749616276 0.9345762552750961 chr16 90354753 38859761 0.43007987637352074 2.277789642110415 chr17 81195210 33419326 0.41159233407980594 1.290491002040699 chr18 78077248 33690561 0.43150292643511207 1.9625858956015487 chr19 59128983 21807040 0.3688045843778507 1.5865373922985173 chr20 63025520 29378067 0.46612970428486744 1.1512693363055617 chr21 48129895 14996228 0.31157824050935495 1.0830180245995222 chr22 51304566 14522493 0.28306433778233303 0.86668288221297 chrMT 16571 179236 10.816245247721923 8.233965644539111 chrX 155270560 68554605 0.44151708475837276 1.1721721188566891 chrY 59373566 2417428 0.04071556018717151 1.1012099804650026