BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124858.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 = 134,103,648 number of mapped reads = 131,381,175 (97.97%) number of supplementary alignments = 21,730,575 (16.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 65,718,108 number of mapped paired reads (second in pair) = 65,663,067 number of mapped paired reads (both in pair) = 130,795,226 number of mapped paired reads (singletons) = 585,949 number of mapped bases = 14,106,787,210 bp number of sequenced bases = 14,092,619,714 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,138,443 duplication rate = 35.92% >>>>>>> Insert size mean insert size = 715,353.1935 std insert size = 8,206,147.6375 median insert size = 113 >>>>>>> Mapping quality mean mapping quality = 46.6383 >>>>>>> ACTG content number of A's = 4,055,054,788 bp (28.77%) number of C's = 2,984,396,421 bp (21.18%) number of T's = 3,975,231,846 bp (28.21%) number of G's = 3,075,906,102 bp (21.83%) number of N's = 2,030,557 bp (0.01%) GC percentage = 43% >>>>>>> Mismatches and indels general error rate = 0.0158 number of mismatches = 209,865,081 number of insertions = 4,837,739 mapped reads with insertion percentage = 3.49% number of deletions = 5,622,019 mapped reads with deletion percentage = 4.05% homopolymer indels = 37.22% >>>>>>> Coverage mean coverageData = 4.5569X std coverageData = 197.0583X There is a 64.7% of reference with a coverageData >= 1X There is a 56.66% of reference with a coverageData >= 2X There is a 40.37% of reference with a coverageData >= 3X There is a 34.4% of reference with a coverageData >= 4X There is a 26.8% of reference with a coverageData >= 5X There is a 23.15% of reference with a coverageData >= 6X There is a 19.36% of reference with a coverageData >= 7X There is a 16.96% of reference with a coverageData >= 8X There is a 14.64% of reference with a coverageData >= 9X There is a 12.85% of reference with a coverageData >= 10X There is a 11.18% of reference with a coverageData >= 11X There is a 9.76% of reference with a coverageData >= 12X There is a 8.46% of reference with a coverageData >= 13X There is a 7.33% of reference with a coverageData >= 14X There is a 6.3% of reference with a coverageData >= 15X There is a 5.41% of reference with a coverageData >= 16X There is a 4.63% of reference with a coverageData >= 17X There is a 3.95% of reference with a coverageData >= 18X There is a 3.36% of reference with a coverageData >= 19X There is a 2.85% of reference with a coverageData >= 20X There is a 2.42% of reference with a coverageData >= 21X There is a 2.06% of reference with a coverageData >= 22X There is a 1.75% of reference with a coverageData >= 23X There is a 1.49% of reference with a coverageData >= 24X There is a 1.28% of reference with a coverageData >= 25X There is a 1.1% of reference with a coverageData >= 26X There is a 0.95% of reference with a coverageData >= 27X There is a 0.82% of reference with a coverageData >= 28X There is a 0.72% of reference with a coverageData >= 29X There is a 0.63% of reference with a coverageData >= 30X There is a 0.56% of reference with a coverageData >= 31X There is a 0.5% of reference with a coverageData >= 32X There is a 0.45% of reference with a coverageData >= 33X There is a 0.4% of reference with a coverageData >= 34X There is a 0.36% of reference with a coverageData >= 35X There is a 0.33% of reference with a coverageData >= 36X There is a 0.31% of reference with a coverageData >= 37X There is a 0.28% of reference with a coverageData >= 38X There is a 0.26% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1378300974 5.529779498523296 588.5140528430993 chr2 243199373 1089659796 4.480520580947386 93.07580396005358 chr3 198022430 858930498 4.337541449218657 30.0825200290893 chr4 191154276 766983355 4.012378750031205 95.54495245637368 chr5 180915260 737517113 4.0765887465767126 13.67891947039824 chr6 171115067 703454698 4.111003842811808 52.84009670394582 chr7 159138663 926721000 5.823355446941263 149.24331568672648 chr8 146364022 852049693 5.82144219157902 66.83323381284765 chr9 141213431 621054304 4.397983248491427 148.53526152292693 chr10 135534747 853937421 6.300505515386398 290.9594802531819 chr11 135006516 515006856 3.8146814780406597 46.10846240199307 chr12 133851895 636950884 4.758624328777714 34.36916558286896 chr13 115169878 302841856 2.6295231119373073 4.8045376969377065 chr14 107349540 381019704 3.5493370907784048 11.662236033173256 chr15 102531392 324130780 3.1612833267688396 24.124775540014898 chr16 90354753 535862828 5.930654561138582 59.09431646425088 chr17 81195210 407773365 5.0221357269720714 58.19394889799303 chr18 78077248 299535780 3.8364028916592963 189.4301539017006 chr19 59128983 475400677 8.040061791693592 299.60657098387327 chr20 63025520 255786970 4.058466633833406 31.895152676071024 chr21 48129895 160718948 3.3392748519397353 52.433657234493495 chr22 51304566 154404756 3.009571428788619 25.376812322759964 chrMT 16571 32511395 1961.9452658258404 843.623439435211 chrX 155270560 553941688 3.56758994106803 30.810553460754267 chrY 59373566 282291871 4.754504235100179 121.47659836346423