BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617393.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 27,743,712 (86.7%) number of supplementary alignments = 378,337 (1.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,081,403 number of mapped paired reads (second in pair) = 13,662,309 number of mapped paired reads (both in pair) = 26,967,420 number of mapped paired reads (singletons) = 776,292 number of mapped bases = 2,713,873,832 bp number of sequenced bases = 2,713,301,799 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,174,940 duplication rate = 3.89% >>>>>>> Insert size mean insert size = 48,123.5893 std insert size = 2,095,551.579 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 53.6946 >>>>>>> ACTG content number of A's = 812,369,850 bp (29.94%) number of C's = 542,047,174 bp (19.98%) number of T's = 801,248,965 bp (29.53%) number of G's = 555,640,225 bp (20.48%) number of N's = 1,995,585 bp (0.07%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0173 number of mismatches = 46,490,639 number of insertions = 247,442 mapped reads with insertion percentage = 0.88% number of deletions = 258,514 mapped reads with deletion percentage = 0.91% homopolymer indels = 43.05% >>>>>>> Coverage mean coverageData = 0.8767X std coverageData = 2.6798X There is a 28.5% of reference with a coverageData >= 1X There is a 16.02% of reference with a coverageData >= 2X There is a 10.07% of reference with a coverageData >= 3X There is a 6.87% of reference with a coverageData >= 4X There is a 4.93% of reference with a coverageData >= 5X There is a 3.67% of reference with a coverageData >= 6X There is a 2.81% of reference with a coverageData >= 7X There is a 2.21% of reference with a coverageData >= 8X There is a 1.76% of reference with a coverageData >= 9X There is a 1.43% of reference with a coverageData >= 10X There is a 1.18% of reference with a coverageData >= 11X There is a 0.98% of reference with a coverageData >= 12X There is a 0.83% of reference with a coverageData >= 13X There is a 0.7% of reference with a coverageData >= 14X There is a 0.6% of reference with a coverageData >= 15X There is a 0.52% of reference with a coverageData >= 16X There is a 0.45% of reference with a coverageData >= 17X There is a 0.39% of reference with a coverageData >= 18X There is a 0.34% of reference with a coverageData >= 19X There is a 0.3% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.17% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.1% of reference with a coverageData >= 30X There is a 0.09% of reference with a coverageData >= 31X There is a 0.08% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 174208522 0.6989291392778516 2.517442318307899 chr2 243199373 271375398 1.1158556646443327 2.8332917336569596 chr3 198022430 229440104 1.1586571480816592 3.108472704659739 chr4 191154276 132084451 0.6909835017240211 2.119860119059719 chr5 180915260 174389116 0.9639270672910621 2.653044665832118 chr6 171115067 125076556 0.7309499870049433 2.396557131688117 chr7 159138663 203208865 1.2769295730478771 2.976497414694166 chr8 146364022 120467858 0.8230701531282052 2.9708389734375267 chr9 141213431 108443743 0.7679421300938436 2.394936077835616 chr10 135534747 86752197 0.6400734787220284 2.1943547238425616 chr11 135006516 201012847 1.4889121870236248 3.5285679222165625 chr12 133851895 129291151 0.965926937381051 2.552192861139256 chr13 115169878 118681184 1.0304880586918743 2.570274921915902 chr14 107349540 78598125 0.7321701145622049 2.651461846076648 chr15 102531392 62105335 0.6057201973811104 2.1624236250644624 chr16 90354753 67593726 0.7480926432281875 3.0088977175662763 chr17 81195210 82434947 1.0152685977411722 3.321720576491935 chr18 78077248 39087800 0.5006298377729707 1.8394654082873934 chr19 59128983 37816950 0.6395670630763258 2.0985834707091997 chr20 63025520 91139102 1.4460666409416376 4.283686637480667 chr21 48129895 37082199 0.7704608331266877 2.3228775671591335 chr22 51304566 21465453 0.4183926436489103 1.882884810869039 chrMT 16571 170462 10.286766037052683 4.942966468570786 chrX 155270560 119753060 0.771254125701614 2.3583673531523157 chrY 59373566 2194681 0.03696394115859573 0.5045580566293456