BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617418.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 27,153,437 (84.85%) number of supplementary alignments = 381,000 (1.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,181,414 number of mapped paired reads (second in pair) = 12,972,023 number of mapped paired reads (both in pair) = 25,664,688 number of mapped paired reads (singletons) = 1,488,749 number of mapped bases = 2,633,156,273 bp number of sequenced bases = 2,632,584,256 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,137,225 duplication rate = 3.79% >>>>>>> Insert size mean insert size = 56,042.1696 std insert size = 2,263,755.296 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 53.4435 >>>>>>> ACTG content number of A's = 787,929,323 bp (29.93%) number of C's = 525,584,750 bp (19.96%) number of T's = 782,510,645 bp (29.72%) number of G's = 535,975,704 bp (20.36%) number of N's = 583,834 bp (0.02%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0176 number of mismatches = 45,786,313 number of insertions = 222,900 mapped reads with insertion percentage = 0.81% number of deletions = 258,035 mapped reads with deletion percentage = 0.93% homopolymer indels = 43.43% >>>>>>> Coverage mean coverageData = 0.8506X std coverageData = 2.6121X There is a 28.11% of reference with a coverageData >= 1X There is a 15.66% of reference with a coverageData >= 2X There is a 9.79% of reference with a coverageData >= 3X There is a 6.64% of reference with a coverageData >= 4X There is a 4.74% of reference with a coverageData >= 5X There is a 3.52% of reference with a coverageData >= 6X There is a 2.69% of reference with a coverageData >= 7X There is a 2.1% of reference with a coverageData >= 8X There is a 1.68% of reference with a coverageData >= 9X There is a 1.36% of reference with a coverageData >= 10X There is a 1.11% of reference with a coverageData >= 11X There is a 0.93% of reference with a coverageData >= 12X There is a 0.78% of reference with a coverageData >= 13X There is a 0.66% of reference with a coverageData >= 14X There is a 0.56% of reference with a coverageData >= 15X There is a 0.48% of reference with a coverageData >= 16X There is a 0.42% of reference with a coverageData >= 17X There is a 0.36% of reference with a coverageData >= 18X There is a 0.32% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.17% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.14% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.11% of reference with a coverageData >= 28X There is a 0.1% of reference with a coverageData >= 29X There is a 0.09% of reference with a coverageData >= 30X There is a 0.08% of reference with a coverageData >= 31X There is a 0.08% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 169318693 0.6793110176443653 2.4391902456005874 chr2 243199373 262657569 1.0800092358790745 2.797406218730488 chr3 198022430 222977473 1.1260212946583879 3.040972141748265 chr4 191154276 128140270 0.6703500056676733 2.0647222069925872 chr5 180915260 169474094 0.9367595304011392 2.5872017176972046 chr6 171115067 121374372 0.709314346935913 2.345480051563056 chr7 159138663 196900421 1.2372883954667886 2.90823158426277 chr8 146364022 116809040 0.7980720835889574 2.86669219207924 chr9 141213431 105229925 0.7451835441913454 2.3298335818405316 chr10 135534747 84202199 0.6212591299558039 2.138674405118924 chr11 135006516 194742899 1.4424703693560983 3.416186235832714 chr12 133851895 125421538 0.9370172756986369 2.5071495821811354 chr13 115169878 114887161 0.9975452175090435 2.5003055780967145 chr14 107349540 76314387 0.7108962646696018 2.572262856702868 chr15 102531392 60210133 0.5872360827794086 2.1352632899836794 chr16 90354753 65532652 0.725281734763859 2.921113809205474 chr17 81195210 80232242 0.9881400885594114 3.2351887587147536 chr18 78077248 37772461 0.48378320147759307 1.782926053033955 chr19 59128983 36734063 0.6212530832806645 2.053505743602964 chr20 63025520 88638648 1.406392965896989 4.125980667930672 chr21 48129895 36139171 0.7508674390417848 2.2776918924225247 chr22 51304566 20949258 0.4083312584692754 1.8412845187632174 chrMT 16571 172717 10.422847142598515 5.12632661316031 chrX 155270560 116206313 0.7484117594475089 2.3085819902106754 chrY 59373566 2118574 0.03568210809504014 0.5322996164767271