BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089646.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 12,755,171 number of mapped reads = 9,641,076 (75.59%) number of supplementary alignments = 388 (0%) number of secondary alignments = 0 number of mapped bases = 452,806,432 bp number of sequenced bases = 452,713,387 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 576,508 duplication rate = 4.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.744 >>>>>>> ACTG content number of A's = 133,685,443 bp (29.53%) number of C's = 93,930,781 bp (20.75%) number of T's = 129,279,805 bp (28.56%) number of G's = 95,702,435 bp (21.14%) number of N's = 114,923 bp (0.03%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 3,030,959 number of insertions = 20,052 mapped reads with insertion percentage = 0.21% number of deletions = 63,066 mapped reads with deletion percentage = 0.65% homopolymer indels = 44.44% >>>>>>> Coverage mean coverageData = 0.1463X std coverageData = 0.8459X There is a 10% of reference with a coverageData >= 1X There is a 2.71% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.1% 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 0.02% 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 38597531 0.1548543022486592 1.0386239059131617 chr2 243199373 43785249 0.18003849458937543 1.3032185745276725 chr3 198022430 42126971 0.21273838019258728 0.6796755682043619 chr4 191154276 20725116 0.10842088617468332 0.4707350497294178 chr5 180915260 19325806 0.10682242061836023 0.4522661068559665 chr6 171115067 28375006 0.16582412348294262 0.6975663633118089 chr7 159138663 29602483 0.186016914066948 1.356891543551481 chr8 146364022 36013908 0.24605710821474966 1.3403535371753665 chr9 141213431 15769123 0.11166871938689742 0.7961687344498166 chr10 135534747 18530263 0.13671964872594627 0.7911669379022995 chr11 135006516 21629835 0.16021326703964422 0.8079393653110435 chr12 133851895 15243081 0.11388020319024994 0.4899901137600163 chr13 115169878 12958795 0.1125189609039961 0.4590978708516447 chr14 107349540 14917166 0.13895882553385883 0.5849720236291148 chr15 102531392 11258111 0.10980160105502128 0.4569477137628253 chr16 90354753 8776598 0.09713487900298948 0.49416153223166615 chr17 81195210 10417824 0.12830589390679573 0.5653940406598935 chr18 78077248 21867719 0.28007799403995387 1.2078641782713322 chr19 59128983 7468993 0.12631695356573272 1.0454900587240294 chr20 63025520 9933579 0.15761201176920078 0.5811716092340145 chr21 48129895 6952133 0.14444521435170388 0.5905483897133424 chr22 51304566 3487206 0.06797067535860259 0.34863937270196976 chrMT 16571 229588 13.854806589825598 11.262434238298464 chrX 155270560 13777167 0.08873006576391558 0.6096618916965646 chrY 59373566 1037181 0.017468733476443035 0.2777180203358194