BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927017.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 28,581,286 number of mapped reads = 28,110,623 (98.35%) number of supplementary alignments = 248,483 (0.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,092,908 number of mapped paired reads (second in pair) = 14,017,715 number of mapped paired reads (both in pair) = 27,881,736 number of mapped paired reads (singletons) = 228,887 number of mapped bases = 2,659,597,170 bp number of sequenced bases = 2,657,594,458 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,854,613 duplication rate = 4.94% >>>>>>> Insert size mean insert size = 99,441.3403 std insert size = 3,099,138.3377 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 53.4668 >>>>>>> ACTG content number of A's = 764,083,651 bp (28.75%) number of C's = 528,549,355 bp (19.89%) number of T's = 772,796,800 bp (29.08%) number of G's = 591,590,759 bp (22.26%) number of N's = 573,893 bp (0.02%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 24,206,058 number of insertions = 431,017 mapped reads with insertion percentage = 1.51% number of deletions = 1,403,292 mapped reads with deletion percentage = 4.86% homopolymer indels = 53.03% >>>>>>> Coverage mean coverageData = 0.8591X std coverageData = 3.9452X There is a 34.69% of reference with a coverageData >= 1X There is a 19.19% of reference with a coverageData >= 2X There is a 11.11% of reference with a coverageData >= 3X There is a 6.77% of reference with a coverageData >= 4X There is a 4.25% of reference with a coverageData >= 5X There is a 2.73% of reference with a coverageData >= 6X There is a 1.79% of reference with a coverageData >= 7X There is a 1.19% of reference with a coverageData >= 8X There is a 0.8% of reference with a coverageData >= 9X There is a 0.54% of reference with a coverageData >= 10X There is a 0.38% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 217576296 0.8729217810053119 5.644674265065421 chr2 243199373 233809884 0.96139180424614 6.1399324710029894 chr3 198022430 178562032 0.9017262943394847 1.7679260634080831 chr4 191154276 163259152 0.8540701019944749 2.6604357733798225 chr5 180915260 163273664 0.9024869654444849 1.736037526868085 chr6 171115067 151918486 0.8878147825521407 1.8073451613775875 chr7 159138663 138977052 0.873307902555396 2.442293137194101 chr8 146364022 133431517 0.9116415029917666 2.0714381425995225 chr9 141213431 111532461 0.7898148229257315 4.50625992517017 chr10 135534747 132719375 0.9792276736237977 9.426855668950331 chr11 135006516 127479620 0.9442479057825623 4.778453387004613 chr12 133851895 117123992 0.875026774929111 1.7416804570859343 chr13 115169878 81405706 0.7068315727485619 1.5371068806483061 chr14 107349540 81391198 0.7581886051863846 1.6512931227479801 chr15 102531392 78065622 0.7613826407428468 1.6494357915704496 chr16 90354753 83226844 0.9211119640822879 5.340170712637047 chr17 81195210 69972707 0.8617836815743195 2.3324244591866137 chr18 78077248 71792654 0.9195079980277994 4.70797650395143 chr19 59128983 42001409 0.7103353866241874 3.134607974892383 chr20 63025520 62049923 0.9845206037173513 2.037117333104944 chr21 48129895 34573136 0.7183297615754201 2.2210687611141546 chr22 51304566 32824452 0.6397959199187067 1.6043448111725402 chrMT 16571 37772 2.2794037776839056 2.7140476273104683 chrX 155270560 148019865 0.9533028347421431 2.3291816814356374 chrY 59373566 4572351 0.07700987675222337 2.308635375937385