BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472600.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 8,580,196 number of mapped reads = 7,860,822 (91.62%) number of supplementary alignments = 258,555 (3.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,966,655 number of mapped paired reads (second in pair) = 3,894,167 number of mapped paired reads (both in pair) = 7,679,798 number of mapped paired reads (singletons) = 181,024 number of mapped bases = 638,057,791 bp number of sequenced bases = 637,788,517 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,215,223 duplication rate = 13.48% >>>>>>> Insert size mean insert size = 240,774.8446 std insert size = 4,698,867.4963 median insert size = 125 >>>>>>> Mapping quality mean mapping quality = 50.469 >>>>>>> ACTG content number of A's = 164,309,434 bp (25.76%) number of C's = 128,392,502 bp (20.13%) number of T's = 189,056,178 bp (29.64%) number of G's = 155,628,275 bp (24.4%) number of N's = 402,128 bp (0.06%) GC percentage = 44.53% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 7,349,404 number of insertions = 59,850 mapped reads with insertion percentage = 0.75% number of deletions = 143,070 mapped reads with deletion percentage = 1.78% homopolymer indels = 42.39% >>>>>>> Coverage mean coverageData = 0.2061X std coverageData = 2.0207X There is a 11.49% of reference with a coverageData >= 1X There is a 5.17% of reference with a coverageData >= 2X There is a 1.71% of reference with a coverageData >= 3X There is a 0.81% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% 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 0.01% 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% 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 39600728 0.15887915480860526 2.2958164464144795 chr2 243199373 59846835 0.24608137044827003 3.2159642665161674 chr3 198022430 31760422 0.16038800251062468 0.5903854818454812 chr4 191154276 30346084 0.15875179271427858 1.0595238360939756 chr5 180915260 27764287 0.15346569990834383 0.5996863233763187 chr6 171115067 40112547 0.2344185564909956 1.076506398696569 chr7 159138663 49958038 0.31392772226570737 3.2422298546521864 chr8 146364022 29493007 0.20150448584967146 1.6486332472928071 chr9 141213431 20422795 0.14462360170258876 1.990430887471482 chr10 135534747 34347614 0.2534229395802096 1.920988115789544 chr11 135006516 31148319 0.2307171529409736 1.7380795846940953 chr12 133851895 29989493 0.22404982013889307 0.7293540998029947 chr13 115169878 34319580 0.29799093822084277 0.8701782298799641 chr14 107349540 15437069 0.1438019110282168 5.214757554016253 chr15 102531392 18106900 0.17659859723741975 0.6414294879589322 chr16 90354753 22505110 0.24907499885479184 1.1234082232101086 chr17 81195210 18538564 0.22832090710769762 1.3290806518007257 chr18 78077248 13162617 0.1685845407870933 3.144888930243678 chr19 59128983 10729196 0.18145409333355184 1.6772371812100066 chr20 63025520 25528199 0.40504543238992713 1.4007727899563693 chr21 48129895 9235953 0.19189638788948116 0.8510114121760138 chr22 51304566 6083608 0.11857829574077286 0.5130804588415451 chrMT 16571 433756 26.175607989861806 16.115085110615006 chrX 155270560 37677166 0.24265492441065453 1.04082728509547 chrY 59373566 1509904 0.025430576293834196 0.844997390996309