BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472693.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 83,263,976 number of mapped reads = 82,567,370 (99.16%) number of supplementary alignments = 540,530 (0.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 41,406,658 number of mapped paired reads (second in pair) = 41,160,712 number of mapped paired reads (both in pair) = 82,130,210 number of mapped paired reads (singletons) = 437,160 number of mapped bases = 8,127,205,303 bp number of sequenced bases = 8,125,611,795 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,014,169 duplication rate = 52.16% >>>>>>> Insert size mean insert size = 21,892.9009 std insert size = 1,452,805.4194 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 54.993 >>>>>>> ACTG content number of A's = 2,182,673,739 bp (26.86%) number of C's = 1,885,722,427 bp (23.21%) number of T's = 2,191,479,563 bp (26.97%) number of G's = 1,864,101,736 bp (22.94%) number of N's = 1,634,330 bp (0.02%) GC percentage = 46.15% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 45,473,366 number of insertions = 521,469 mapped reads with insertion percentage = 0.63% number of deletions = 444,730 mapped reads with deletion percentage = 0.53% homopolymer indels = 44.58% >>>>>>> Coverage mean coverageData = 2.6253X std coverageData = 115.2702X There is a 12.15% of reference with a coverageData >= 1X There is a 5.95% of reference with a coverageData >= 2X There is a 2.78% of reference with a coverageData >= 3X There is a 1.83% of reference with a coverageData >= 4X There is a 1.21% of reference with a coverageData >= 5X There is a 0.97% of reference with a coverageData >= 6X There is a 0.8% of reference with a coverageData >= 7X There is a 0.72% of reference with a coverageData >= 8X There is a 0.65% of reference with a coverageData >= 9X There is a 0.61% of reference with a coverageData >= 10X There is a 0.58% of reference with a coverageData >= 11X There is a 0.56% of reference with a coverageData >= 12X There is a 0.54% of reference with a coverageData >= 13X There is a 0.53% of reference with a coverageData >= 14X There is a 0.51% of reference with a coverageData >= 15X There is a 0.5% of reference with a coverageData >= 16X There is a 0.49% of reference with a coverageData >= 17X There is a 0.48% of reference with a coverageData >= 18X There is a 0.48% of reference with a coverageData >= 19X There is a 0.47% of reference with a coverageData >= 20X There is a 0.46% of reference with a coverageData >= 21X There is a 0.45% of reference with a coverageData >= 22X There is a 0.45% of reference with a coverageData >= 23X There is a 0.44% of reference with a coverageData >= 24X There is a 0.44% of reference with a coverageData >= 25X There is a 0.43% of reference with a coverageData >= 26X There is a 0.43% of reference with a coverageData >= 27X There is a 0.42% of reference with a coverageData >= 28X There is a 0.42% of reference with a coverageData >= 29X There is a 0.41% of reference with a coverageData >= 30X There is a 0.41% of reference with a coverageData >= 31X There is a 0.4% of reference with a coverageData >= 32X There is a 0.4% of reference with a coverageData >= 33X There is a 0.4% of reference with a coverageData >= 34X There is a 0.39% of reference with a coverageData >= 35X There is a 0.39% of reference with a coverageData >= 36X There is a 0.39% of reference with a coverageData >= 37X There is a 0.38% of reference with a coverageData >= 38X There is a 0.38% of reference with a coverageData >= 39X There is a 0.38% of reference with a coverageData >= 40X There is a 0.37% of reference with a coverageData >= 41X There is a 0.37% of reference with a coverageData >= 42X There is a 0.37% of reference with a coverageData >= 43X There is a 0.37% of reference with a coverageData >= 44X There is a 0.36% of reference with a coverageData >= 45X There is a 0.36% 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 0.35% of reference with a coverageData >= 49X There is a 0.35% of reference with a coverageData >= 50X There is a 0.35% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1056093286 4.2370738406304715 156.4716341367676 chr2 243199373 545032179 2.241092040150942 107.9786233892525 chr3 198022430 657841395 3.32205495609765 76.61338429997242 chr4 191154276 238102722 1.2456050002250538 47.90749812615707 chr5 180915260 415764138 2.2981153607495575 162.7787799599317 chr6 171115067 570650683 3.334894425164793 92.91120656141133 chr7 159138663 507470925 3.1888600509355793 169.7698409448674 chr8 146364022 338579971 2.3132732099969213 65.77948943555685 chr9 141213431 311639094 2.2068658185920005 58.51370662118787 chr10 135534747 149550309 1.1034093640946554 40.51615818804422 chr11 135006516 341271278 2.527813383466617 88.63720160888172 chr12 133851895 340253779 2.542016898602743 90.26510485746981 chr13 115169878 228456397 1.983647121689232 96.42650751155925 chr14 107349540 172875522 1.6103983491685199 47.07950445832544 chr15 102531392 183689839 1.7915473048488408 67.83174333466793 chr16 90354753 531498240 5.882349542807117 222.44686450556597 chr17 81195210 522416141 6.434075864820104 295.74557261273924 chr18 78077248 85035837 1.0891244143236196 35.210033475791114 chr19 59128983 247736704 4.189767715098363 104.52447729860926 chr20 63025520 206708250 3.2797547723525327 114.88562747574585 chr21 48129895 56243773 1.1685829150468747 74.02821582483837 chr22 51304566 110688912 2.157486567569834 77.33515864857435 chrMT 16571 25709 1.5514452959990344 1.6178057265423782 chrX 155270560 301506602 1.9418143529591185 68.93221789606945 chrY 59373566 8073618 0.13598000834243307 8.872794253231557