BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365367.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 291,200,364 number of mapped reads = 266,965,642 (91.68%) number of supplementary alignments = 11,082,382 (3.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 133,834,382 number of mapped paired reads (second in pair) = 133,131,260 number of mapped paired reads (both in pair) = 261,902,612 number of mapped paired reads (singletons) = 5,063,030 number of mapped bases = 34,005,176,274 bp number of sequenced bases = 33,985,750,834 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,046,915 duplication rate = 38.6% >>>>>>> Insert size mean insert size = 139,092.3174 std insert size = 3,627,427.3793 median insert size = 154 >>>>>>> Mapping quality mean mapping quality = 53.2574 >>>>>>> ACTG content number of A's = 9,512,492,142 bp (27.99%) number of C's = 7,054,932,024 bp (20.76%) number of T's = 9,754,638,918 bp (28.7%) number of G's = 7,662,286,004 bp (22.55%) number of N's = 1,401,746 bp (0%) GC percentage = 43.3% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 351,894,760 number of insertions = 3,330,680 mapped reads with insertion percentage = 1.19% number of deletions = 9,205,454 mapped reads with deletion percentage = 3.35% homopolymer indels = 43.32% >>>>>>> Coverage mean coverageData = 10.9847X std coverageData = 99.6522X There is a 37.46% of reference with a coverageData >= 1X There is a 32.64% of reference with a coverageData >= 2X There is a 28% of reference with a coverageData >= 3X There is a 26.46% of reference with a coverageData >= 4X There is a 24.85% of reference with a coverageData >= 5X There is a 23.91% of reference with a coverageData >= 6X There is a 22.85% of reference with a coverageData >= 7X There is a 22.09% of reference with a coverageData >= 8X There is a 21.25% of reference with a coverageData >= 9X There is a 20.59% of reference with a coverageData >= 10X There is a 19.88% of reference with a coverageData >= 11X There is a 19.29% of reference with a coverageData >= 12X There is a 18.66% of reference with a coverageData >= 13X There is a 18.12% of reference with a coverageData >= 14X There is a 17.56% of reference with a coverageData >= 15X There is a 17.06% of reference with a coverageData >= 16X There is a 16.55% of reference with a coverageData >= 17X There is a 16.09% of reference with a coverageData >= 18X There is a 15.62% of reference with a coverageData >= 19X There is a 15.19% of reference with a coverageData >= 20X There is a 14.75% of reference with a coverageData >= 21X There is a 14.35% of reference with a coverageData >= 22X There is a 13.94% of reference with a coverageData >= 23X There is a 13.56% of reference with a coverageData >= 24X There is a 13.18% of reference with a coverageData >= 25X There is a 12.82% of reference with a coverageData >= 26X There is a 12.46% of reference with a coverageData >= 27X There is a 12.13% of reference with a coverageData >= 28X There is a 11.79% of reference with a coverageData >= 29X There is a 11.47% of reference with a coverageData >= 30X There is a 11.16% of reference with a coverageData >= 31X There is a 10.86% of reference with a coverageData >= 32X There is a 10.56% of reference with a coverageData >= 33X There is a 10.27% of reference with a coverageData >= 34X There is a 9.99% of reference with a coverageData >= 35X There is a 9.72% of reference with a coverageData >= 36X There is a 9.46% of reference with a coverageData >= 37X There is a 9.21% of reference with a coverageData >= 38X There is a 8.96% of reference with a coverageData >= 39X There is a 8.72% of reference with a coverageData >= 40X There is a 8.48% of reference with a coverageData >= 41X There is a 8.26% of reference with a coverageData >= 42X There is a 8.04% of reference with a coverageData >= 43X There is a 7.82% of reference with a coverageData >= 44X There is a 7.61% of reference with a coverageData >= 45X There is a 7.41% of reference with a coverageData >= 46X There is a 7.22% of reference with a coverageData >= 47X There is a 7.03% of reference with a coverageData >= 48X There is a 6.84% of reference with a coverageData >= 49X There is a 6.67% of reference with a coverageData >= 50X There is a 6.49% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2750612659 11.035529813183494 183.6359472058703 chr2 243199373 2973324108 12.225870779691524 127.3891750367938 chr3 198022430 2260392430 11.414830279579945 31.520988470444514 chr4 191154276 2217350864 11.599797349027128 57.69918471832294 chr5 180915260 2053093793 11.348372674588092 34.59522120955758 chr6 171115067 1985269769 11.601957699026 56.662892782984414 chr7 159138663 1875419443 11.784813367446727 129.12107050042144 chr8 146364022 1783128900 12.182836161744723 59.830054001571916 chr9 141213431 1493237827 10.574332883392657 152.81041445038247 chr10 135534747 1691615179 12.481044281581903 128.9018666747055 chr11 135006516 1611977967 11.940001229274001 144.52543049452393 chr12 133851895 1551112153 11.588271895590271 32.35131528829012 chr13 115169878 1081520784 9.390656678476294 28.340970585876583 chr14 107349540 1067916774 9.948033070286096 53.7880313858084 chr15 102531392 974532989 9.504727966630941 29.006715930758265 chr16 90354753 1019084678 11.278705814181132 44.173864393668374 chr17 81195210 964733894 11.881660186604604 82.48266334472916 chr18 78077248 969240037 12.413860142714046 170.9837402235806 chr19 59128983 688777408 11.648727460778414 109.96921529624302 chr20 63025520 756494694 12.002990122096573 38.140525883622 chr21 48129895 477023040 9.911158958481002 54.04583345225127 chr22 51304566 429105176 8.36387887970829 38.88388417295407 chrMT 16571 25256045 1524.1110977008027 1048.0379375131845 chrX 155270560 1041503755 6.707670501091772 42.401183513808604 chrY 59373566 263451908 4.437191931507028 62.95947515382371