BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618622.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 32,841,948 number of mapped reads = 30,295,170 (92.25%) number of supplementary alignments = 67,329 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,419,899 number of mapped paired reads (second in pair) = 14,875,271 number of mapped paired reads (both in pair) = 29,356,292 number of mapped paired reads (singletons) = 938,878 number of mapped bases = 2,889,653,462 bp number of sequenced bases = 2,887,814,241 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,869,412 duplication rate = 31.51% >>>>>>> Insert size mean insert size = 65,419.81 std insert size = 2,596,426.9217 median insert size = 230 >>>>>>> Mapping quality mean mapping quality = 53.9089 >>>>>>> ACTG content number of A's = 769,268,198 bp (26.64%) number of C's = 658,699,727 bp (22.81%) number of T's = 772,833,100 bp (26.76%) number of G's = 686,904,243 bp (23.79%) number of N's = 108,973 bp (0%) GC percentage = 46.6% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 35,149,497 number of insertions = 516,328 mapped reads with insertion percentage = 1.67% number of deletions = 1,323,951 mapped reads with deletion percentage = 4.27% homopolymer indels = 52.74% >>>>>>> Coverage mean coverageData = 0.9334X std coverageData = 4.6301X There is a 18.13% of reference with a coverageData >= 1X There is a 12.11% of reference with a coverageData >= 2X There is a 9.01% of reference with a coverageData >= 3X There is a 7.07% of reference with a coverageData >= 4X There is a 5.71% of reference with a coverageData >= 5X There is a 4.71% of reference with a coverageData >= 6X There is a 3.94% of reference with a coverageData >= 7X There is a 3.34% of reference with a coverageData >= 8X There is a 2.86% of reference with a coverageData >= 9X There is a 2.47% of reference with a coverageData >= 10X There is a 2.15% of reference with a coverageData >= 11X There is a 1.88% of reference with a coverageData >= 12X There is a 1.66% of reference with a coverageData >= 13X There is a 1.47% of reference with a coverageData >= 14X There is a 1.3% of reference with a coverageData >= 15X There is a 1.16% of reference with a coverageData >= 16X There is a 1.04% of reference with a coverageData >= 17X There is a 0.94% of reference with a coverageData >= 18X There is a 0.85% of reference with a coverageData >= 19X There is a 0.77% of reference with a coverageData >= 20X There is a 0.7% of reference with a coverageData >= 21X There is a 0.64% of reference with a coverageData >= 22X There is a 0.58% of reference with a coverageData >= 23X There is a 0.53% of reference with a coverageData >= 24X There is a 0.49% of reference with a coverageData >= 25X There is a 0.45% of reference with a coverageData >= 26X There is a 0.41% of reference with a coverageData >= 27X There is a 0.38% of reference with a coverageData >= 28X There is a 0.35% of reference with a coverageData >= 29X There is a 0.33% of reference with a coverageData >= 30X There is a 0.3% of reference with a coverageData >= 31X There is a 0.28% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 266797724 1.0703994354341047 5.263946402045464 chr2 243199373 232857781 0.9574768969490723 5.482619334056423 chr3 198022430 176597802 0.8918070644825438 3.7226811144832372 chr4 191154276 129684448 0.6784281822709527 3.782462928747555 chr5 180915260 150408178 0.8313736386858688 3.636358535084813 chr6 171115067 142059170 0.8301967353932661 3.5715692250565585 chr7 159138663 140347311 0.8819183745435891 4.203359983028105 chr8 146364022 133899926 0.9148418044975561 4.050368310836405 chr9 141213431 133407497 0.9447224393266105 4.712979939525271 chr10 135534747 142755661 1.0532772160632726 4.423814794180391 chr11 135006516 152102818 1.126633161913459 4.940606358171807 chr12 133851895 129822369 0.969895637263858 4.218153796589033 chr13 115169878 74089649 0.6433075235175642 3.0990169099072036 chr14 107349540 85269608 0.7943174046204576 3.6684155671017296 chr15 102531392 101012101 0.9851821869345146 4.297971999949926 chr16 90354753 108856069 1.204763063211517 9.459393744505523 chr17 81195210 112915031 1.3906612348191476 5.295983018848445 chr18 78077248 70836103 0.9072566568944643 3.976652271247445 chr19 59128983 75916184 1.283908163954046 5.487311004421833 chr20 63025520 89806948 1.4249299014113648 5.216759566675567 chr21 48129895 37519631 0.7795494047930086 6.198383042723876 chr22 51304566 61027065 1.1895055305603794 5.163817986329462 chrMT 16571 17451 1.0531048216764227 5.429511272023467 chrX 155270560 137193879 0.8835794692825221 3.580094923007881 chrY 59373566 4453058 0.07500068296386307 2.999883697454354