BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617663.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 = 30,126,935 (94.15%) number of supplementary alignments = 140,153 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,110,465 number of mapped paired reads (second in pair) = 15,016,470 number of mapped paired reads (both in pair) = 29,492,024 number of mapped paired reads (singletons) = 634,911 number of mapped bases = 2,924,028,737 bp number of sequenced bases = 2,922,256,651 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,894,127 duplication rate = 10.7% >>>>>>> Insert size mean insert size = 32,497.0964 std insert size = 1,662,878.0319 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 52.6436 >>>>>>> ACTG content number of A's = 870,399,693 bp (29.79%) number of C's = 582,934,976 bp (19.95%) number of T's = 868,501,329 bp (29.72%) number of G's = 598,419,880 bp (20.48%) number of N's = 2,000,773 bp (0.07%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0152 number of mismatches = 43,503,507 number of insertions = 454,201 mapped reads with insertion percentage = 1.48% number of deletions = 1,070,232 mapped reads with deletion percentage = 3.48% homopolymer indels = 47.61% >>>>>>> Coverage mean coverageData = 0.9445X std coverageData = 10.5738X There is a 33.26% of reference with a coverageData >= 1X There is a 19.23% of reference with a coverageData >= 2X There is a 11.74% of reference with a coverageData >= 3X There is a 7.49% of reference with a coverageData >= 4X There is a 4.92% of reference with a coverageData >= 5X There is a 3.33% of reference with a coverageData >= 6X There is a 2.31% of reference with a coverageData >= 7X There is a 1.64% of reference with a coverageData >= 8X There is a 1.18% of reference with a coverageData >= 9X There is a 0.87% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% 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 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 179060064 0.71839365246757 10.255059613905706 chr2 243199373 301901553 1.241374717688931 12.046808522609409 chr3 198022430 244765112 1.2360474113967796 2.4611554679431786 chr4 191154276 163621829 0.8559674019533835 8.307231221594714 chr5 180915260 193704714 1.0706930637028629 2.3114424245231047 chr6 171115067 142039622 0.8300824964758948 5.690463531202495 chr7 159138663 228611736 1.4365568472822974 13.382758316439876 chr8 146364022 130145432 0.889190049724105 4.081058512462485 chr9 141213431 120106562 0.8505321423710752 20.46307272966958 chr10 135534747 123764263 0.913155229485174 21.41777272147764 chr11 135006516 160718897 1.1904528889553745 11.913283651661741 chr12 133851895 124482084 0.9299986675571533 2.149697148350602 chr13 115169878 125725973 1.0916567351056845 2.2788126588424276 chr14 107349540 83851413 0.7811064025053112 2.447433862769868 chr15 102531392 62505763 0.6096256159284368 1.569890306477231 chr16 90354753 80920738 0.8955891672904025 16.72944579639848 chr17 81195210 72134272 0.8884055106206389 12.727818209692064 chr18 78077248 53997585 0.6915918066169545 18.155418300773903 chr19 59128983 30941258 0.5232841227795174 6.044297232279247 chr20 63025520 78940886 1.2525225654623715 3.0255550043588437 chr21 48129895 42766136 0.8885566029179993 4.372325443282299 chr22 51304566 18813147 0.366695373663233 1.2511936841637383 chrMT 16571 3111223 187.75107114839176 133.79980570783678 chrX 155270560 145612986 0.9378016412126033 4.332600335477438 chrY 59373566 11785489 0.19849724033756033 17.55172858882843