BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472714.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 = 40,268,014 number of mapped reads = 39,948,143 (99.21%) number of supplementary alignments = 144,354 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 20,027,599 number of mapped paired reads (second in pair) = 19,920,544 number of mapped paired reads (both in pair) = 39,757,732 number of mapped paired reads (singletons) = 190,411 number of mapped bases = 3,930,740,684 bp number of sequenced bases = 3,930,182,611 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,110,398 duplication rate = 47.57% >>>>>>> Insert size mean insert size = 24,496.8851 std insert size = 1,533,442.1765 median insert size = 229 >>>>>>> Mapping quality mean mapping quality = 55.2582 >>>>>>> ACTG content number of A's = 1,081,569,992 bp (27.52%) number of C's = 888,956,002 bp (22.62%) number of T's = 1,074,025,812 bp (27.33%) number of G's = 884,862,538 bp (22.51%) number of N's = 768,267 bp (0.02%) GC percentage = 45.13% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 22,939,190 number of insertions = 229,407 mapped reads with insertion percentage = 0.57% number of deletions = 227,483 mapped reads with deletion percentage = 0.56% homopolymer indels = 44.81% >>>>>>> Coverage mean coverageData = 1.2697X std coverageData = 37.9251X There is a 11.29% of reference with a coverageData >= 1X There is a 5.29% of reference with a coverageData >= 2X There is a 2.27% of reference with a coverageData >= 3X There is a 1.43% of reference with a coverageData >= 4X There is a 0.91% of reference with a coverageData >= 5X There is a 0.73% of reference with a coverageData >= 6X There is a 0.61% of reference with a coverageData >= 7X There is a 0.55% of reference with a coverageData >= 8X There is a 0.51% of reference with a coverageData >= 9X There is a 0.48% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.45% of reference with a coverageData >= 12X There is a 0.43% of reference with a coverageData >= 13X There is a 0.42% of reference with a coverageData >= 14X There is a 0.41% of reference with a coverageData >= 15X There is a 0.4% of reference with a coverageData >= 16X There is a 0.39% of reference with a coverageData >= 17X There is a 0.39% of reference with a coverageData >= 18X There is a 0.38% of reference with a coverageData >= 19X There is a 0.37% of reference with a coverageData >= 20X There is a 0.37% of reference with a coverageData >= 21X There is a 0.36% of reference with a coverageData >= 22X There is a 0.36% of reference with a coverageData >= 23X There is a 0.35% of reference with a coverageData >= 24X There is a 0.35% of reference with a coverageData >= 25X There is a 0.34% of reference with a coverageData >= 26X There is a 0.34% of reference with a coverageData >= 27X There is a 0.33% of reference with a coverageData >= 28X There is a 0.33% of reference with a coverageData >= 29X There is a 0.32% of reference with a coverageData >= 30X There is a 0.32% of reference with a coverageData >= 31X There is a 0.32% of reference with a coverageData >= 32X There is a 0.31% of reference with a coverageData >= 33X There is a 0.31% of reference with a coverageData >= 34X There is a 0.31% of reference with a coverageData >= 35X There is a 0.3% of reference with a coverageData >= 36X There is a 0.3% of reference with a coverageData >= 37X There is a 0.3% of reference with a coverageData >= 38X There is a 0.29% of reference with a coverageData >= 39X There is a 0.29% of reference with a coverageData >= 40X There is a 0.29% of reference with a coverageData >= 41X There is a 0.29% of reference with a coverageData >= 42X There is a 0.28% of reference with a coverageData >= 43X There is a 0.28% of reference with a coverageData >= 44X There is a 0.28% of reference with a coverageData >= 45X There is a 0.27% of reference with a coverageData >= 46X There is a 0.27% of reference with a coverageData >= 47X There is a 0.27% of reference with a coverageData >= 48X There is a 0.27% of reference with a coverageData >= 49X There is a 0.27% of reference with a coverageData >= 50X There is a 0.26% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 422185495 1.6938192302437634 51.766902968741064 chr2 243199373 252413668 1.0378878238308615 35.35810868340653 chr3 198022430 502769600 2.5389527842881234 53.78040652646771 chr4 191154276 155645749 0.814241523951052 27.963063503381335 chr5 180915260 154200029 0.8523329043663868 22.828808118044872 chr6 171115067 217999224 1.2739919857554098 34.908166167764 chr7 159138663 159530668 1.0024632920285375 29.014780259864192 chr8 146364022 237009844 1.6193176489779708 47.02041617993487 chr9 141213431 187517931 1.3279043620149702 31.939792673318237 chr10 135534747 105770138 0.7803913043789428 23.918538087846656 chr11 135006516 232421566 1.7215581357569438 55.48326514681332 chr12 133851895 244401840 1.8259124385202017 51.93897273932457 chr13 115169878 73309634 0.6365347890704547 21.54502922288252 chr14 107349540 139301486 1.2976439954935997 48.79598799485481 chr15 102531392 72760090 0.7096372006731363 19.918104629716293 chr16 90354753 113418033 1.255252537738662 32.705093190665664 chr17 81195210 172132851 2.119987755435327 37.990212866198924 chr18 78077248 84102392 1.0771690108749734 33.20868953083392 chr19 59128983 67305865 1.1382888997093017 22.489302321382127 chr20 63025520 100583954 1.5959242224419568 45.44482780694229 chr21 48129895 15333030 0.3185760118529243 10.28382754447009 chr22 51304566 33878427 0.6603394130651061 19.21294341066854 chrMT 16571 11866 0.7160702431959447 1.8979380938772505 chrX 155270560 178164888 1.1474479643790814 31.982892009723653 chrY 59373566 8572416 0.1443810196611738 10.254619510458973