BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960906.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 = 158,816,452 number of mapped reads = 155,759,564 (98.08%) number of supplementary alignments = 321,545 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 78,180,609 number of mapped paired reads (second in pair) = 77,578,955 number of mapped paired reads (both in pair) = 154,664,358 number of mapped paired reads (singletons) = 1,095,206 number of mapped bases = 15,354,702,799 bp number of sequenced bases = 15,350,187,732 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,066,686 duplication rate = 5.03% >>>>>>> Insert size mean insert size = 20,180.4235 std insert size = 1,331,691.2641 median insert size = 150 >>>>>>> Mapping quality mean mapping quality = 53.6445 >>>>>>> ACTG content number of A's = 4,534,060,607 bp (29.54%) number of C's = 3,130,848,204 bp (20.4%) number of T's = 4,520,645,660 bp (29.45%) number of G's = 3,158,031,514 bp (20.57%) number of N's = 6,601,747 bp (0.04%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 142,536,820 number of insertions = 1,719,909 mapped reads with insertion percentage = 1.07% number of deletions = 1,883,694 mapped reads with deletion percentage = 1.17% homopolymer indels = 40.96% >>>>>>> Coverage mean coverageData = 4.96X std coverageData = 52.3658X There is a 89.06% of reference with a coverageData >= 1X There is a 83.52% of reference with a coverageData >= 2X There is a 74.3% of reference with a coverageData >= 3X There is a 62.62% of reference with a coverageData >= 4X There is a 49.81% of reference with a coverageData >= 5X There is a 37.54% of reference with a coverageData >= 6X There is a 26.87% of reference with a coverageData >= 7X There is a 18.36% of reference with a coverageData >= 8X There is a 12.03% of reference with a coverageData >= 9X There is a 7.61% of reference with a coverageData >= 10X There is a 4.68% of reference with a coverageData >= 11X There is a 2.83% of reference with a coverageData >= 12X There is a 1.7% of reference with a coverageData >= 13X There is a 1.04% of reference with a coverageData >= 14X There is a 0.66% of reference with a coverageData >= 15X There is a 0.44% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.2% of reference with a coverageData >= 19X There is a 0.18% of reference with a coverageData >= 20X There is a 0.16% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.13% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.11% of reference with a coverageData >= 25X There is a 0.11% of reference with a coverageData >= 26X There is a 0.1% of reference with a coverageData >= 27X There is a 0.09% of reference with a coverageData >= 28X There is a 0.09% of reference with a coverageData >= 29X There is a 0.08% of reference with a coverageData >= 30X There is a 0.08% of reference with a coverageData >= 31X There is a 0.08% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1250550552 5.017241469580933 130.32727049364226 chr2 243199373 1319906126 5.427259576035174 33.548242295408464 chr3 198022430 1017891395 5.140283325479846 9.218804583256658 chr4 191154276 1036221946 5.420867205711893 40.95127099190052 chr5 180915260 928071141 5.129866551887331 5.439265514296982 chr6 171115067 883610405 5.163837530449612 16.13230163469047 chr7 159138663 820908803 5.158449791676332 33.46745368748724 chr8 146364022 777207893 5.310102048165908 58.15691135634845 chr9 141213431 640194816 4.533526389568426 46.786380935650364 chr10 135534747 788687687 5.819081117257702 109.65478471284155 chr11 135006516 691958982 5.125374704136503 21.507209395211973 chr12 133851895 679173507 5.0740671770093355 4.970982624762962 chr13 115169878 492071598 4.272572017485336 3.482856555386133 chr14 107349540 453787503 4.227195598602472 5.121579207966377 chr15 102531392 425394033 4.148915026921706 3.5466606710865523 chr16 90354753 476448234 5.27308435008394 43.9271742382119 chr17 81195210 404898365 4.986727234278968 20.327641126618573 chr18 78077248 421020739 5.39236140853735 55.782017351543686 chr19 59128983 292218197 4.942046728589937 64.28463336469683 chr20 63025520 313874816 4.98012259161051 16.342475301818407 chr21 48129895 210147825 4.366263940530101 21.699111341504516 chr22 51304566 175744164 3.4255072735631367 4.390255296346217 chrMT 16571 11816803 713.1013819322914 109.750772055535 chrX 155270560 794438266 5.116477109376047 16.75008633421906 chrY 59373566 48459003 0.8161713413002682 45.2618079469165