BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617501.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,402,783 (95.01%) number of supplementary alignments = 187,344 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,346,854 number of mapped paired reads (second in pair) = 15,055,929 number of mapped paired reads (both in pair) = 29,786,524 number of mapped paired reads (singletons) = 616,259 number of mapped bases = 2,953,839,096 bp number of sequenced bases = 2,952,085,336 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,283,178 duplication rate = 9.97% >>>>>>> Insert size mean insert size = 49,989.1149 std insert size = 2,102,043.2442 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 52.6184 >>>>>>> ACTG content number of A's = 871,674,438 bp (29.53%) number of C's = 595,590,381 bp (20.18%) number of T's = 871,297,818 bp (29.51%) number of G's = 610,411,809 bp (20.68%) number of N's = 3,110,890 bp (0.11%) GC percentage = 40.85% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 35,584,534 number of insertions = 443,698 mapped reads with insertion percentage = 1.43% number of deletions = 1,028,793 mapped reads with deletion percentage = 3.31% homopolymer indels = 47.39% >>>>>>> Coverage mean coverageData = 0.9542X std coverageData = 9.6069X There is a 38.11% of reference with a coverageData >= 1X There is a 20.51% of reference with a coverageData >= 2X There is a 11.55% of reference with a coverageData >= 3X There is a 6.85% of reference with a coverageData >= 4X There is a 4.22% of reference with a coverageData >= 5X There is a 2.7% of reference with a coverageData >= 6X There is a 1.78% of reference with a coverageData >= 7X There is a 1.22% of reference with a coverageData >= 8X There is a 0.85% of reference with a coverageData >= 9X There is a 0.62% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 189967333 0.7621539005112449 9.360608856832618 chr2 243199373 305091620 1.2544918033156278 11.358243094436162 chr3 198022430 243876977 1.231562389169752 2.2672601159776877 chr4 191154276 152676546 0.7987085049564887 6.148515396584144 chr5 180915260 189021490 1.0448067785989972 2.091528295704106 chr6 171115067 139284904 0.8139838673586821 5.349261283723353 chr7 159138663 227866440 1.431873535345713 13.095667369415763 chr8 146364022 131368831 0.8975486544090733 3.835549788118259 chr9 141213431 122187568 0.865268743452597 17.920089603801653 chr10 135534747 124969532 0.9220479232532156 18.535031157952787 chr11 135006516 166525474 1.2334624945065615 12.5553726537494 chr12 133851895 129009053 0.9638193990454897 2.083767371357133 chr13 115169878 125327576 1.0881975233142125 2.192341679424116 chr14 107349540 86096766 0.802022682165196 2.2525271453024427 chr15 102531392 66873100 0.6522207364550361 1.6948688324798924 chr16 90354753 79728555 0.8823946981516291 14.706048752396665 chr17 81195210 82581977 1.0170794188474912 13.420427803032206 chr18 78077248 53064501 0.679641026794387 16.983247333171718 chr19 59128983 35266882 0.5964398542082147 5.804872693392888 chr20 63025520 87132374 1.3824935359517858 2.820733704871143 chr21 48129895 42474592 0.8824991619034283 3.8091303404689874 chr22 51304566 22226143 0.4332195890712729 1.2669692851187573 chrMT 16571 2052882 123.88401424174764 93.19772823430705 chrX 155270560 138882569 0.8944552592584196 4.123939224241068 chrY 59373566 10285411 0.17323215856699595 13.463829457922069