BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124826.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 30,363,196 number of mapped reads = 30,128,659 (99.23%) number of supplementary alignments = 130,037 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,073,207 number of mapped paired reads (second in pair) = 15,055,452 number of mapped paired reads (both in pair) = 30,031,026 number of mapped paired reads (singletons) = 97,633 number of mapped bases = 2,754,432,843 bp number of sequenced bases = 2,752,896,476 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,857,884 duplication rate = 5.09% >>>>>>> Insert size mean insert size = 64,911.5592 std insert size = 2,411,077.2434 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 52.517 >>>>>>> ACTG content number of A's = 806,064,007 bp (29.28%) number of C's = 550,450,093 bp (20%) number of T's = 806,731,212 bp (29.3%) number of G's = 589,630,584 bp (21.42%) number of N's = 20,580 bp (0%) GC percentage = 41.41% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 19,684,058 number of insertions = 476,981 mapped reads with insertion percentage = 1.55% number of deletions = 887,039 mapped reads with deletion percentage = 2.88% homopolymer indels = 46.99% >>>>>>> Coverage mean coverageData = 0.8898X std coverageData = 8.6815X There is a 33.01% of reference with a coverageData >= 1X There is a 19.23% of reference with a coverageData >= 2X There is a 11.33% of reference with a coverageData >= 3X There is a 7.04% of reference with a coverageData >= 4X There is a 4.5% of reference with a coverageData >= 5X There is a 2.96% of reference with a coverageData >= 6X There is a 1.99% of reference with a coverageData >= 7X There is a 1.36% of reference with a coverageData >= 8X There is a 0.95% of reference with a coverageData >= 9X There is a 0.68% of reference with a coverageData >= 10X There is a 0.49% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 214478315 0.8604926003373929 8.722980758240622 chr2 243199373 224651190 0.9237326035375922 10.295411186745337 chr3 198022430 203109595 1.0256898423072578 2.214496988612785 chr4 191154276 125436723 0.656206733246187 8.415772743694 chr5 180915260 126661160 0.7001131911150005 1.7444911258608438 chr6 171115067 172215503 1.0064309708039911 4.462854139532848 chr7 159138663 127795483 0.8030448452366349 15.63475724627484 chr8 146364022 171391634 1.1709956562959167 3.840039551564884 chr9 141213431 155952711 1.104375907416342 12.705785454578947 chr10 135534747 170401823 1.2572556246406688 20.40612354063769 chr11 135006516 120261844 0.890785478828296 3.536809279758908 chr12 133851895 106187974 0.7933243978353837 1.7357730081018738 chr13 115169878 92067105 0.7994026441531873 1.7234310784968425 chr14 107349540 87219461 0.8124809943293656 2.3480545647994027 chr15 102531392 64164143 0.6257999793858255 1.5575897572606852 chr16 90354753 89914652 0.9951291881678875 14.895015780928997 chr17 81195210 79659660 0.9810881701026453 7.007741198564972 chr18 78077248 63154322 0.8088697234820571 13.10582355182724 chr19 59128983 38489513 0.650941569551433 5.018813184342723 chr20 63025520 79850351 1.266952672504725 3.0976689998069884 chr21 48129895 50814589 1.0557801757099199 4.111248519610941 chr22 51304566 35852740 0.6988216214517827 1.8199200446466917 chrMT 16571 699933 42.23842858004949 23.553776202098806 chrX 155270560 146666734 0.9445881691931812 3.100173446930849 chrY 59373566 7335685 0.12355136290786374 8.568314918917062