BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618608.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 = 54,416,916 number of mapped reads = 50,699,438 (93.17%) number of supplementary alignments = 168,570 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 26,034,507 number of mapped paired reads (second in pair) = 24,664,931 number of mapped paired reads (both in pair) = 48,313,168 number of mapped paired reads (singletons) = 2,386,270 number of mapped bases = 4,732,723,836 bp number of sequenced bases = 4,729,603,239 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,313,233 duplication rate = 37.51% >>>>>>> Insert size mean insert size = 98,981.6427 std insert size = 3,168,655.4288 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 53.7696 >>>>>>> ACTG content number of A's = 1,247,334,208 bp (26.37%) number of C's = 1,080,310,310 bp (22.84%) number of T's = 1,268,433,189 bp (26.82%) number of G's = 1,130,036,225 bp (23.89%) number of N's = 3,489,307 bp (0.07%) GC percentage = 46.73% >>>>>>> Mismatches and indels general error rate = 0.0155 number of mismatches = 71,892,286 number of insertions = 876,542 mapped reads with insertion percentage = 1.7% number of deletions = 2,296,861 mapped reads with deletion percentage = 4.42% homopolymer indels = 51.93% >>>>>>> Coverage mean coverageData = 1.5288X std coverageData = 7.5903X There is a 20.28% of reference with a coverageData >= 1X There is a 14.76% of reference with a coverageData >= 2X There is a 11.7% of reference with a coverageData >= 3X There is a 9.75% of reference with a coverageData >= 4X There is a 8.27% of reference with a coverageData >= 5X There is a 7.16% of reference with a coverageData >= 6X There is a 6.26% of reference with a coverageData >= 7X There is a 5.53% of reference with a coverageData >= 8X There is a 4.92% of reference with a coverageData >= 9X There is a 4.4% of reference with a coverageData >= 10X There is a 3.96% of reference with a coverageData >= 11X There is a 3.58% of reference with a coverageData >= 12X There is a 3.25% of reference with a coverageData >= 13X There is a 2.96% of reference with a coverageData >= 14X There is a 2.7% of reference with a coverageData >= 15X There is a 2.48% of reference with a coverageData >= 16X There is a 2.28% of reference with a coverageData >= 17X There is a 2.1% of reference with a coverageData >= 18X There is a 1.94% of reference with a coverageData >= 19X There is a 1.79% of reference with a coverageData >= 20X There is a 1.66% of reference with a coverageData >= 21X There is a 1.54% of reference with a coverageData >= 22X There is a 1.44% of reference with a coverageData >= 23X There is a 1.34% of reference with a coverageData >= 24X There is a 1.25% of reference with a coverageData >= 25X There is a 1.17% of reference with a coverageData >= 26X There is a 1.09% of reference with a coverageData >= 27X There is a 1.03% of reference with a coverageData >= 28X There is a 0.96% of reference with a coverageData >= 29X There is a 0.91% of reference with a coverageData >= 30X There is a 0.85% of reference with a coverageData >= 31X There is a 0.8% of reference with a coverageData >= 32X There is a 0.76% of reference with a coverageData >= 33X There is a 0.72% of reference with a coverageData >= 34X There is a 0.68% of reference with a coverageData >= 35X There is a 0.64% of reference with a coverageData >= 36X There is a 0.61% of reference with a coverageData >= 37X There is a 0.57% of reference with a coverageData >= 38X There is a 0.54% of reference with a coverageData >= 39X There is a 0.52% of reference with a coverageData >= 40X There is a 0.49% of reference with a coverageData >= 41X There is a 0.47% of reference with a coverageData >= 42X There is a 0.44% of reference with a coverageData >= 43X There is a 0.42% of reference with a coverageData >= 44X There is a 0.4% of reference with a coverageData >= 45X There is a 0.38% of reference with a coverageData >= 46X There is a 0.36% of reference with a coverageData >= 47X There is a 0.35% of reference with a coverageData >= 48X There is a 0.33% of reference with a coverageData >= 49X There is a 0.32% of reference with a coverageData >= 50X There is a 0.3% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 420489715 1.6870157166027682 8.933855190263907 chr2 243199373 396109584 1.6287442648957817 8.276326910600948 chr3 198022430 295994554 1.4947526600900716 6.728472180755459 chr4 191154276 223508472 1.1692569827734327 6.289318020479463 chr5 180915260 256334256 1.4168747069760728 6.347780257868183 chr6 171115067 251490481 1.4697155861792113 6.774223235071067 chr7 159138663 234056287 1.4707694697673814 7.103363797973899 chr8 146364022 231411448 1.5810678391988982 6.910246729310751 chr9 141213431 206341494 1.4612030352835206 7.747186168981936 chr10 135534747 245588935 1.8119998040059793 8.037008830527625 chr11 135006516 236364802 1.7507658815519689 8.045214106302874 chr12 133851895 211768735 1.582112341405402 7.554712009652858 chr13 115169878 124308725 1.0793510174596173 5.500893483672724 chr14 107349540 145908437 1.3591901465064498 6.379029545733551 chr15 102531392 160907660 1.5693501947189012 7.889060984816866 chr16 90354753 177282398 1.9620705288187772 12.77758912061456 chr17 81195210 161246996 1.9859175929220456 8.13776272337581 chr18 78077248 119329102 1.5283466702105075 6.442481047570404 chr19 59128983 104631171 1.7695411909925798 8.207013769987695 chr20 63025520 142281842 2.2575274587183096 9.261338501111574 chr21 48129895 62227482 1.2929070798928608 8.500589677787863 chr22 51304566 90555425 1.7650558626692212 8.408569378064714 chrMT 16571 188327 11.364854263472331 42.15136279849504 chrX 155270560 227993167 1.4683605636509587 6.318256477138931 chrY 59373566 6404341 0.10786519037781898 3.8854863926631786