BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504622.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 529,249,188 number of mapped reads = 483,330,488 (91.32%) number of supplementary alignments = 4,956,749 (0.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 242,805,082 number of mapped paired reads (second in pair) = 240,525,406 number of mapped paired reads (both in pair) = 472,651,096 number of mapped paired reads (singletons) = 10,679,392 number of mapped bases = 46,346,260,636 bp number of sequenced bases = 46,305,927,782 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 179,979,487 duplication rate = 26.71% >>>>>>> Insert size mean insert size = 106,072.3817 std insert size = 3,050,182.1155 median insert size = 328 >>>>>>> Mapping quality mean mapping quality = 52.219 >>>>>>> ACTG content number of A's = 12,411,655,007 bp (26.8%) number of C's = 10,669,718,573 bp (23.04%) number of T's = 12,490,028,087 bp (26.97%) number of G's = 10,683,888,174 bp (23.07%) number of N's = 50,637,941 bp (0.11%) GC percentage = 46.11% >>>>>>> Mismatches and indels general error rate = 0.0155 number of mismatches = 664,133,264 number of insertions = 13,575,049 mapped reads with insertion percentage = 2.61% number of deletions = 12,266,140 mapped reads with deletion percentage = 2.37% homopolymer indels = 34.49% >>>>>>> Coverage mean coverageData = 14.9712X std coverageData = 367.3502X There is a 87.13% of reference with a coverageData >= 1X There is a 81.96% of reference with a coverageData >= 2X There is a 76.49% of reference with a coverageData >= 3X There is a 71.21% of reference with a coverageData >= 4X There is a 66.2% of reference with a coverageData >= 5X There is a 61.55% of reference with a coverageData >= 6X There is a 57.23% of reference with a coverageData >= 7X There is a 53.25% of reference with a coverageData >= 8X There is a 49.58% of reference with a coverageData >= 9X There is a 46.18% of reference with a coverageData >= 10X There is a 43.04% of reference with a coverageData >= 11X There is a 40.12% of reference with a coverageData >= 12X There is a 37.41% of reference with a coverageData >= 13X There is a 34.89% of reference with a coverageData >= 14X There is a 32.53% of reference with a coverageData >= 15X There is a 30.34% of reference with a coverageData >= 16X There is a 28.29% of reference with a coverageData >= 17X There is a 26.38% of reference with a coverageData >= 18X There is a 24.6% of reference with a coverageData >= 19X There is a 22.93% of reference with a coverageData >= 20X There is a 21.37% of reference with a coverageData >= 21X There is a 19.92% of reference with a coverageData >= 22X There is a 18.57% of reference with a coverageData >= 23X There is a 17.3% of reference with a coverageData >= 24X There is a 16.12% of reference with a coverageData >= 25X There is a 15.02% of reference with a coverageData >= 26X There is a 13.99% of reference with a coverageData >= 27X There is a 13.04% of reference with a coverageData >= 28X There is a 12.15% of reference with a coverageData >= 29X There is a 11.33% of reference with a coverageData >= 30X There is a 10.56% of reference with a coverageData >= 31X There is a 9.85% of reference with a coverageData >= 32X There is a 9.18% of reference with a coverageData >= 33X There is a 8.57% of reference with a coverageData >= 34X There is a 7.99% of reference with a coverageData >= 35X There is a 7.46% of reference with a coverageData >= 36X There is a 6.97% of reference with a coverageData >= 37X There is a 6.51% of reference with a coverageData >= 38X There is a 6.08% of reference with a coverageData >= 39X There is a 5.69% of reference with a coverageData >= 40X There is a 5.32% of reference with a coverageData >= 41X There is a 4.98% of reference with a coverageData >= 42X There is a 4.66% of reference with a coverageData >= 43X There is a 4.37% of reference with a coverageData >= 44X There is a 4.1% of reference with a coverageData >= 45X There is a 3.85% of reference with a coverageData >= 46X There is a 3.61% of reference with a coverageData >= 47X There is a 3.4% of reference with a coverageData >= 48X There is a 3.19% of reference with a coverageData >= 49X There is a 3.01% of reference with a coverageData >= 50X There is a 2.83% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3570258235 14.323969267061525 108.9347646985039 chr2 243199373 3648254813 15.00108642549831 351.3521080933567 chr3 198022430 2475195132 12.499569528563002 33.07329969732885 chr4 191154276 3510760911 18.36611235942219 1036.9889269848834 chr5 180915260 2408682006 13.313868636620262 46.42538969474927 chr6 171115067 1985731047 11.604653417223627 46.23823098991696 chr7 159138663 2279098376 14.32146238403423 52.4823181969255 chr8 146364022 2177409548 14.876672000718866 280.9654905572929 chr9 141213431 1691470082 11.97811050989902 126.80226233982566 chr10 135534747 3056197917 22.54918376761348 800.4506040679058 chr11 135006516 1985998474 14.710389785927074 44.85220419781989 chr12 133851895 1851577366 13.833030649285915 26.37923080662234 chr13 115169878 1034303671 8.980678706631954 20.21361209426467 chr14 107349540 1235611192 11.510167551719364 43.11979971666273 chr15 102531392 1349563831 13.162445224580585 22.529842897864068 chr16 90354753 2076818372 22.985159087314422 278.796672419559 chr17 81195210 1586371952 19.537752929021305 104.61106246080128 chr18 78077248 1053212619 13.489366569374987 417.75635044435614 chr19 59128983 1543152836 26.09807843304188 59.89145780337359 chr20 63025520 1184114939 18.787864645940246 249.56386736676492 chr21 48129895 771173361 16.022751784519787 335.7959435680342 chr22 51304566 853603912 16.63797159886315 42.455734361326385 chrMT 16571 17586343 1061.2722829038682 494.197113862388 chrX 155270560 2266006312 14.59392116573805 30.266922654264334 chrY 59373566 734107389 12.364212535255167 871.3478055865315