BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008778.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 = 1,093,255 number of mapped reads = 957,588 (87.59%) number of supplementary alignments = 10,394 (0.95%) number of secondary alignments = 0 number of mapped bases = 63,230,572 bp number of sequenced bases = 63,198,858 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,297 duplication rate = 3.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5101 >>>>>>> ACTG content number of A's = 17,164,083 bp (27.16%) number of C's = 12,169,865 bp (19.26%) number of T's = 19,489,645 bp (30.84%) number of G's = 14,282,046 bp (22.6%) number of N's = 93,219 bp (0.15%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 540,608 number of insertions = 4,485 mapped reads with insertion percentage = 0.46% number of deletions = 18,007 mapped reads with deletion percentage = 1.86% homopolymer indels = 44.86% >>>>>>> Coverage mean coverageData = 0.0204X std coverageData = 0.2141X There is a 1.63% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.06% 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 5384819 0.02160403443889514 0.2609424647767577 chr2 243199373 5950545 0.024467764561218668 0.29244319879346076 chr3 198022430 5486378 0.02770584120192849 0.20467042579823727 chr4 191154276 3795174 0.019853984328344294 0.17164164694219186 chr5 180915260 2536812 0.014022100733791058 0.14238971760386346 chr6 171115067 3196194 0.018678624016200747 0.17370824127952417 chr7 159138663 3422230 0.021504704988001565 0.25945681298282924 chr8 146364022 3898215 0.026633696906743925 0.31608268165001197 chr9 141213431 1765003 0.012498832352568504 0.15257311597048748 chr10 135534747 3877791 0.028611046877890286 0.27715790764798576 chr11 135006516 2639868 0.019553633989043907 0.1978642303570863 chr12 133851895 2455349 0.018343774662286254 0.1631601424744192 chr13 115169878 1788225 0.015526846351265562 0.15081453190273464 chr14 107349540 1701380 0.01584897336309033 0.15384492180864467 chr15 102531392 1627528 0.015873460491007477 0.1524115026164593 chr16 90354753 1479386 0.016373084435303584 0.17093998819465217 chr17 81195210 2227488 0.027433736546774126 0.21819855073793806 chr18 78077248 609614 0.007807831546521721 0.2077938879643251 chr19 59128983 1695597 0.028676241564986837 0.23794186874603393 chr20 63025520 1388028 0.022023269304243743 0.18103259652641765 chr21 48129895 696389 0.01446894908040003 0.14910462945134653 chr22 51304566 1146799 0.022352766808318776 0.18115973280864414 chrMT 16571 71375 4.307223462675759 3.4056535417840634 chrX 155270560 4211779 0.027125419010532326 0.20998140867322077 chrY 59373566 178606 0.003008173704776297 0.08153902274951894