BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21672007.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 217,146,730 number of mapped reads = 215,149,128 (99.08%) number of supplementary alignments = 1,954,902 (0.9%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 107,684,757 number of mapped paired reads (second in pair) = 107,464,371 number of mapped paired reads (both in pair) = 214,438,848 number of mapped paired reads (singletons) = 710,280 number of mapped bases = 31,609,817,392 bp number of sequenced bases = 31,596,159,783 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,173,495 duplication rate = 19.56% >>>>>>> Insert size mean insert size = 134,471.9833 std insert size = 3,530,247.258 median insert size = 389 >>>>>>> Mapping quality mean mapping quality = 54.3876 >>>>>>> ACTG content number of A's = 9,282,368,690 bp (29.38%) number of C's = 6,529,415,528 bp (20.67%) number of T's = 9,208,737,948 bp (29.15%) number of G's = 6,575,591,761 bp (20.81%) number of N's = 45,856 bp (0%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 251,516,602 number of insertions = 4,546,912 mapped reads with insertion percentage = 1.99% number of deletions = 4,853,222 mapped reads with deletion percentage = 2.16% homopolymer indels = 44.5% >>>>>>> Coverage mean coverageData = 10.2109X std coverageData = 125.157X There is a 92.19% of reference with a coverageData >= 1X There is a 91.69% of reference with a coverageData >= 2X There is a 90.6% of reference with a coverageData >= 3X There is a 88.63% of reference with a coverageData >= 4X There is a 85.5% of reference with a coverageData >= 5X There is a 81.01% of reference with a coverageData >= 6X There is a 75.09% of reference with a coverageData >= 7X There is a 67.9% of reference with a coverageData >= 8X There is a 59.74% of reference with a coverageData >= 9X There is a 51.1% of reference with a coverageData >= 10X There is a 42.48% of reference with a coverageData >= 11X There is a 34.34% of reference with a coverageData >= 12X There is a 27.01% of reference with a coverageData >= 13X There is a 20.71% of reference with a coverageData >= 14X There is a 15.51% of reference with a coverageData >= 15X There is a 11.37% of reference with a coverageData >= 16X There is a 8.19% of reference with a coverageData >= 17X There is a 5.82% of reference with a coverageData >= 18X There is a 4.09% of reference with a coverageData >= 19X There is a 2.87% of reference with a coverageData >= 20X There is a 2.02% of reference with a coverageData >= 21X There is a 1.43% of reference with a coverageData >= 22X There is a 1.04% of reference with a coverageData >= 23X There is a 0.78% of reference with a coverageData >= 24X There is a 0.61% of reference with a coverageData >= 25X There is a 0.49% of reference with a coverageData >= 26X There is a 0.41% of reference with a coverageData >= 27X There is a 0.36% of reference with a coverageData >= 28X There is a 0.32% of reference with a coverageData >= 29X There is a 0.29% of reference with a coverageData >= 30X There is a 0.27% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2631757494 10.558679787602214 310.50468726010945 chr2 243199373 2729204007 11.222084881773112 81.34755358674617 chr3 198022430 2061462305 10.410246480663831 9.040096334219012 chr4 191154276 2055626367 10.753755605236892 81.29351661871834 chr5 180915260 1881777130 10.401428436716726 8.545690479172531 chr6 171115067 1837006940 10.73550665179005 88.95870981798319 chr7 159138663 1713599281 10.767963288720102 67.67088613374713 chr8 146364022 1585353161 10.831576908975622 97.28513526211233 chr9 141213431 1390860860 9.849352502454247 212.4806099987103 chr10 135534747 1662490818 12.266159452085006 215.23444924224597 chr11 135006516 1453677956 10.767465149608038 40.9379546908031 chr12 133851895 1403689466 10.486885269722928 22.627960247902156 chr13 115169878 989699098 8.593384964773515 6.437354940509732 chr14 107349540 953765199 8.884669640875964 9.64415301571895 chr15 102531392 907063062 8.846686310471625 7.375774095843053 chr16 90354753 1041075013 11.52208354772438 73.41349787977968 chr17 81195210 941850542 11.599828881531312 63.41951926322271 chr18 78077248 900524947 11.533769056511828 170.5632487815294 chr19 59128983 702044431 11.873101740985465 139.80905897098546 chr20 63025520 687843301 10.913726709434528 28.580279223525412 chr21 48129895 453136614 9.41486811886874 44.28058953501773 chr22 51304566 422166810 8.228640117528721 23.58344759529144 chrMT 16571 35926311 2168.0231126667068 247.82887678809317 chrX 155270560 850230690 5.47580101469332 17.478828894296615 chrY 59373566 317985589 5.355676110139654 98.23640330105412