BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708528.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,135,226 number of mapped reads = 2,120,332 (67.63%) number of supplementary alignments = 1,082 (0.03%) number of secondary alignments = 0 number of mapped bases = 100,200,986 bp number of sequenced bases = 100,176,620 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,789 duplication rate = 2.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.3673 >>>>>>> ACTG content number of A's = 28,456,809 bp (28.41%) number of C's = 18,524,619 bp (18.49%) number of T's = 32,002,681 bp (31.95%) number of G's = 21,191,167 bp (21.15%) number of N's = 1,344 bp (0%) GC percentage = 39.65% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 549,062 number of insertions = 6,251 mapped reads with insertion percentage = 0.29% number of deletions = 16,219 mapped reads with deletion percentage = 0.76% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.0324X std coverageData = 0.3703X There is a 2.94% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 8138689 0.03265263278922784 0.6238774400550903 chr2 243199373 8690124 0.03573250988603494 0.5178519497067265 chr3 198022430 7038654 0.035544730968102956 0.21637328160008673 chr4 191154276 6767131 0.035401410533971 0.22423157201129656 chr5 180915260 6336599 0.03502523225514531 0.208094204986417 chr6 171115067 6072310 0.035486705562871326 0.29264711627107937 chr7 159138663 5740448 0.036071988364009315 0.45866015086778567 chr8 146364022 5281676 0.03608589001469227 0.7381758354024468 chr9 141213431 4251035 0.030103616702011865 0.2705184802367315 chr10 135534747 4684113 0.03456023716191391 0.26356103423911886 chr11 135006516 4698301 0.03480054992308668 0.3352607554355406 chr12 133851895 4622265 0.034532682559331715 0.20961136513784473 chr13 115169878 3237133 0.028107462265437148 0.22661554490985641 chr14 107349540 3142645 0.02927488091704911 0.20591306800319048 chr15 102531392 2858743 0.027881636484560747 0.19762959407193142 chr16 90354753 2623441 0.029034897588619383 0.20333161518987533 chr17 81195210 2537676 0.031254011166422256 0.26251431432223654 chr18 78077248 2673134 0.03423704175638977 0.45855987282163196 chr19 59128983 1900658 0.03214427009509025 0.428579880542361 chr20 63025520 1958577 0.031075935589266062 0.1986456055524293 chr21 48129895 1297336 0.026954889471502066 0.2095703679842088 chr22 51304566 1042341 0.02031672970394097 0.17115226536866346 chrMT 16571 117608 7.097218031500815 4.631020762296737 chrX 155270560 3661789 0.023583279405960795 0.20984576065746446 chrY 59373566 828560 0.013955031772893681 0.16401423514733263