BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472637.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 = 15,676,068 number of mapped reads = 15,567,450 (99.31%) number of supplementary alignments = 74,406 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,804,594 number of mapped paired reads (second in pair) = 7,762,856 number of mapped paired reads (both in pair) = 15,491,668 number of mapped paired reads (singletons) = 75,782 number of mapped bases = 1,532,122,390 bp number of sequenced bases = 1,531,939,975 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,526,347 duplication rate = 49.29% >>>>>>> Insert size mean insert size = 21,282.8482 std insert size = 1,482,539.3017 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 54.8179 >>>>>>> ACTG content number of A's = 418,161,629 bp (27.3%) number of C's = 349,620,945 bp (22.82%) number of T's = 419,581,986 bp (27.39%) number of G's = 344,296,013 bp (22.47%) number of N's = 279,402 bp (0.02%) GC percentage = 45.3% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 9,040,383 number of insertions = 91,975 mapped reads with insertion percentage = 0.58% number of deletions = 79,972 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.62% >>>>>>> Coverage mean coverageData = 0.4949X std coverageData = 20.0396X There is a 3.12% of reference with a coverageData >= 1X There is a 1.43% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 208501225 0.8365123591808423 27.94771262306212 chr2 243199373 109249738 0.4492188308396667 17.48208888191808 chr3 198022430 125316120 0.6328380072903862 20.14694374328609 chr4 191154276 24889718 0.13020748748513478 5.6265526716467535 chr5 180915260 53592349 0.29622901351715714 13.601731185849507 chr6 171115067 120457664 0.7039570863739311 18.265557820718026 chr7 159138663 61625375 0.3872432621857581 12.55162202360953 chr8 146364022 104492578 0.7139225649319749 27.395529052704152 chr9 141213431 96229016 0.681443792694195 25.921537970959005 chr10 135534747 28677896 0.21159072957136224 11.299591797206308 chr11 135006516 44581674 0.33021868366709056 12.622908193709584 chr12 133851895 47247279 0.35298177138246717 15.463217999670421 chr13 115169878 58882345 0.5112651504241413 23.51096688655916 chr14 107349540 44508025 0.41460843707388034 17.60281630757654 chr15 102531392 30433929 0.2968254737046777 13.499248239301256 chr16 90354753 101052765 1.1184001023166983 41.51764383743132 chr17 81195210 49006755 0.6035670700278994 16.38378649656344 chr18 78077248 11364101 0.14554945635378952 5.657032201328012 chr19 59128983 43441364 0.7346881646856669 28.77553911530565 chr20 63025520 74605594 1.1837362706408452 35.53451078955161 chr21 48129895 10190228 0.21172346210188075 15.95120301006686 chr22 51304566 22732058 0.4430806022216424 21.8372408801707 chrMT 16571 1779 0.1073562247299499 0.4155865305757129 chrX 155270560 60095665 0.3870383735332699 15.09286326425536 chrY 59373566 947150 0.015952385275292375 1.1781074533965934