BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504705.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 = 506,077,902 number of mapped reads = 456,025,762 (90.11%) number of supplementary alignments = 2,331,874 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 229,998,561 number of mapped paired reads (second in pair) = 226,027,201 number of mapped paired reads (both in pair) = 448,458,090 number of mapped paired reads (singletons) = 7,567,672 number of mapped bases = 44,749,250,910 bp number of sequenced bases = 44,739,813,158 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,601,365 duplication rate = 23.44% >>>>>>> Insert size mean insert size = 43,774.5197 std insert size = 1,955,475.0085 median insert size = 409 >>>>>>> Mapping quality mean mapping quality = 53.7673 >>>>>>> ACTG content number of A's = 11,855,873,584 bp (26.5%) number of C's = 10,400,620,563 bp (23.25%) number of T's = 11,873,749,101 bp (26.54%) number of G's = 10,582,390,605 bp (23.65%) number of N's = 27,179,305 bp (0.06%) GC percentage = 46.9% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 349,685,423 number of insertions = 3,085,760 mapped reads with insertion percentage = 0.66% number of deletions = 3,851,812 mapped reads with deletion percentage = 0.82% homopolymer indels = 40.97% >>>>>>> Coverage mean coverageData = 14.4553X std coverageData = 34.2975X There is a 76.29% of reference with a coverageData >= 1X There is a 68.66% of reference with a coverageData >= 2X There is a 62.37% of reference with a coverageData >= 3X There is a 57.28% of reference with a coverageData >= 4X There is a 52.85% of reference with a coverageData >= 5X There is a 48.96% of reference with a coverageData >= 6X There is a 45.49% of reference with a coverageData >= 7X There is a 42.38% of reference with a coverageData >= 8X There is a 39.58% of reference with a coverageData >= 9X There is a 37.04% of reference with a coverageData >= 10X There is a 34.73% of reference with a coverageData >= 11X There is a 32.63% of reference with a coverageData >= 12X There is a 30.7% of reference with a coverageData >= 13X There is a 28.93% of reference with a coverageData >= 14X There is a 27.31% of reference with a coverageData >= 15X There is a 25.81% of reference with a coverageData >= 16X There is a 24.43% of reference with a coverageData >= 17X There is a 23.15% of reference with a coverageData >= 18X There is a 21.97% of reference with a coverageData >= 19X There is a 20.87% of reference with a coverageData >= 20X There is a 19.85% of reference with a coverageData >= 21X There is a 18.89% of reference with a coverageData >= 22X There is a 18.01% of reference with a coverageData >= 23X There is a 17.18% of reference with a coverageData >= 24X There is a 16.4% of reference with a coverageData >= 25X There is a 15.68% of reference with a coverageData >= 26X There is a 15% of reference with a coverageData >= 27X There is a 14.36% of reference with a coverageData >= 28X There is a 13.76% of reference with a coverageData >= 29X There is a 13.19% of reference with a coverageData >= 30X There is a 12.66% of reference with a coverageData >= 31X There is a 12.16% of reference with a coverageData >= 32X There is a 11.68% of reference with a coverageData >= 33X There is a 11.24% of reference with a coverageData >= 34X There is a 10.81% of reference with a coverageData >= 35X There is a 10.41% of reference with a coverageData >= 36X There is a 10.03% of reference with a coverageData >= 37X There is a 9.67% of reference with a coverageData >= 38X There is a 9.32% of reference with a coverageData >= 39X There is a 8.99% of reference with a coverageData >= 40X There is a 8.68% of reference with a coverageData >= 41X There is a 8.39% of reference with a coverageData >= 42X There is a 8.1% of reference with a coverageData >= 43X There is a 7.83% of reference with a coverageData >= 44X There is a 7.58% of reference with a coverageData >= 45X There is a 7.33% of reference with a coverageData >= 46X There is a 7.1% of reference with a coverageData >= 47X There is a 6.87% of reference with a coverageData >= 48X There is a 6.66% of reference with a coverageData >= 49X There is a 6.45% of reference with a coverageData >= 50X There is a 6.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3684900240 14.783915984706814 31.412518798772645 chr2 243199373 3059220864 12.579065588298207 23.85056300266818 chr3 198022430 2609227054 13.17642175181872 24.949944018258826 chr4 191154276 1923643375 10.063302873747904 17.95549671739419 chr5 180915260 2925797015 16.172195839090634 31.155927807479763 chr6 171115067 1351818256 7.900053921026136 15.749818524218863 chr7 159138663 2292675478 14.406778558897406 24.7687385995804 chr8 146364022 2516803236 17.195504753210457 33.822405972205665 chr9 141213431 1071827135 7.590121756902854 27.851096503399873 chr10 135534747 3039929915 22.429155491764778 35.7894286163946 chr11 135006516 2682629904 19.87037354552576 36.25143123839062 chr12 133851895 2036344084 15.213412436185532 35.82852288612515 chr13 115169878 626936774 5.443582861136659 11.01361045360289 chr14 107349540 1292954229 12.044338792695338 23.725869016420507 chr15 102531392 1587079170 15.478958580802258 30.19655180239261 chr16 90354753 2246864508 24.86714238486159 41.89709037107024 chr17 81195210 1746906824 21.514900004569235 40.85857634561024 chr18 78077248 697930890 8.938979124878992 98.63959173298645 chr19 59128983 1922294304 32.510187161514345 60.47969249692718 chr20 63025520 1377182023 21.85118064872769 35.615316569848325 chr21 48129895 571090322 11.865604984178752 25.54657502970852 chr22 51304566 736936591 14.363957215815839 29.753699058645694 chrMT 16571 199134 12.017017681491764 16.99808370292465 chrX 155270560 2664002944 17.157167102379226 28.584206661639673 chrY 59373566 84056641 1.4157249877832838 48.80841719001922