BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504600.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 430,651,964 number of mapped reads = 370,698,643 (86.08%) number of supplementary alignments = 2,055,010 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 185,640,754 number of mapped paired reads (second in pair) = 185,057,889 number of mapped paired reads (both in pair) = 368,508,258 number of mapped paired reads (singletons) = 2,190,385 number of mapped bases = 36,794,473,132 bp number of sequenced bases = 36,784,945,038 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,190,360 duplication rate = 21.96% >>>>>>> Insert size mean insert size = 29,909.255 std insert size = 1,680,108.6665 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 53.9668 >>>>>>> ACTG content number of A's = 9,712,011,763 bp (26.4%) number of C's = 8,604,747,013 bp (23.39%) number of T's = 9,740,247,808 bp (26.48%) number of G's = 8,720,620,262 bp (23.71%) number of N's = 7,318,192 bp (0.02%) GC percentage = 47.1% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 180,592,219 number of insertions = 2,793,346 mapped reads with insertion percentage = 0.73% number of deletions = 3,708,903 mapped reads with deletion percentage = 0.97% homopolymer indels = 40.45% >>>>>>> Coverage mean coverageData = 11.8857X std coverageData = 24.526X There is a 78.63% of reference with a coverageData >= 1X There is a 70.09% of reference with a coverageData >= 2X There is a 62.86% of reference with a coverageData >= 3X There is a 56.81% of reference with a coverageData >= 4X There is a 51.59% of reference with a coverageData >= 5X There is a 47.07% of reference with a coverageData >= 6X There is a 43.1% of reference with a coverageData >= 7X There is a 39.61% of reference with a coverageData >= 8X There is a 36.51% of reference with a coverageData >= 9X There is a 33.75% of reference with a coverageData >= 10X There is a 31.27% of reference with a coverageData >= 11X There is a 29.05% of reference with a coverageData >= 12X There is a 27.04% of reference with a coverageData >= 13X There is a 25.22% of reference with a coverageData >= 14X There is a 23.56% of reference with a coverageData >= 15X There is a 22.05% of reference with a coverageData >= 16X There is a 20.68% of reference with a coverageData >= 17X There is a 19.41% of reference with a coverageData >= 18X There is a 18.26% of reference with a coverageData >= 19X There is a 17.19% of reference with a coverageData >= 20X There is a 16.21% of reference with a coverageData >= 21X There is a 15.3% of reference with a coverageData >= 22X There is a 14.47% of reference with a coverageData >= 23X There is a 13.69% of reference with a coverageData >= 24X There is a 12.97% of reference with a coverageData >= 25X There is a 12.3% of reference with a coverageData >= 26X There is a 11.67% of reference with a coverageData >= 27X There is a 11.09% of reference with a coverageData >= 28X There is a 10.55% of reference with a coverageData >= 29X There is a 10.04% of reference with a coverageData >= 30X There is a 9.56% of reference with a coverageData >= 31X There is a 9.12% of reference with a coverageData >= 32X There is a 8.7% of reference with a coverageData >= 33X There is a 8.31% of reference with a coverageData >= 34X There is a 7.94% of reference with a coverageData >= 35X There is a 7.59% of reference with a coverageData >= 36X There is a 7.26% of reference with a coverageData >= 37X There is a 6.95% of reference with a coverageData >= 38X There is a 6.66% of reference with a coverageData >= 39X There is a 6.39% of reference with a coverageData >= 40X There is a 6.13% of reference with a coverageData >= 41X There is a 5.88% of reference with a coverageData >= 42X There is a 5.65% of reference with a coverageData >= 43X There is a 5.43% of reference with a coverageData >= 44X There is a 5.22% of reference with a coverageData >= 45X There is a 5.02% of reference with a coverageData >= 46X There is a 4.83% of reference with a coverageData >= 47X There is a 4.65% of reference with a coverageData >= 48X There is a 4.48% of reference with a coverageData >= 49X There is a 4.32% of reference with a coverageData >= 50X There is a 4.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3776324307 15.150711728818521 25.49083110356929 chr2 243199373 2524194417 10.37911564434831 18.522447404175924 chr3 198022430 2726871816 13.770519915344943 22.677101220333498 chr4 191154276 1544285428 8.078738599601088 12.76803982733593 chr5 180915260 1499302227 8.287317648052463 13.89012689715258 chr6 171115067 1882200739 10.999620150340121 17.882078980791007 chr7 159138663 2995863134 18.82548890083361 27.843250712137777 chr8 146364022 2813392090 19.22188288867875 47.154024511544954 chr9 141213431 1446004754 10.239852850824084 19.93390742849858 chr10 135534747 1730690532 12.76934933888208 24.097782494452908 chr11 135006516 1873757850 13.879017883847917 23.412056656669478 chr12 133851895 1255004628 9.376069184526674 15.812194673729183 chr13 115169878 837306999 7.270190900089345 13.610253726578442 chr14 107349540 1229547240 11.453679633839139 19.85717665316701 chr15 102531392 819326362 7.990980576953446 14.887129005090973 chr16 90354753 1072252253 11.867137227412929 20.331928705687403 chr17 81195210 1329552756 16.3747683637988 50.293069820521914 chr18 78077248 481906336 6.172173691367811 28.90094973173429 chr19 59128983 1079467224 18.256143928604352 31.596431451382994 chr20 63025520 1652535006 26.22009316226189 39.029827516516804 chr21 48129895 348721508 7.245424242043328 18.29967643332686 chr22 51304566 753545657 14.68769187132389 27.234651975739265 chrMT 16571 245789 14.832478426166194 11.296643772756243 chrX 155270560 1085144700 6.988734374372064 12.306272914577244 chrY 59373566 37029380 0.6236677783510595 14.89305248835256