BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153382.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 = 52,668,876 number of mapped reads = 52,174,893 (99.06%) number of supplementary alignments = 403,680 (0.77%) number of secondary alignments = 0 number of mapped bases = 5,000,153,671 bp number of sequenced bases = 4,999,229,806 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,395,232 duplication rate = 32.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.0831 >>>>>>> ACTG content number of A's = 1,345,138,092 bp (26.91%) number of C's = 1,149,713,830 bp (23%) number of T's = 1,372,652,042 bp (27.46%) number of G's = 1,129,529,667 bp (22.59%) number of N's = 2,196,175 bp (0.04%) GC percentage = 45.59% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 14,880,012 number of insertions = 542,133 mapped reads with insertion percentage = 1.03% number of deletions = 439,564 mapped reads with deletion percentage = 0.83% homopolymer indels = 49.68% >>>>>>> Coverage mean coverageData = 1.6152X std coverageData = 14.3626X There is a 24.91% of reference with a coverageData >= 1X There is a 13.48% of reference with a coverageData >= 2X There is a 7.14% of reference with a coverageData >= 3X There is a 5.04% of reference with a coverageData >= 4X There is a 3.77% of reference with a coverageData >= 5X There is a 3.16% of reference with a coverageData >= 6X There is a 2.76% of reference with a coverageData >= 7X There is a 2.51% of reference with a coverageData >= 8X There is a 2.31% of reference with a coverageData >= 9X There is a 2.16% of reference with a coverageData >= 10X There is a 2.04% of reference with a coverageData >= 11X There is a 1.93% of reference with a coverageData >= 12X There is a 1.84% of reference with a coverageData >= 13X There is a 1.75% of reference with a coverageData >= 14X There is a 1.68% of reference with a coverageData >= 15X There is a 1.61% of reference with a coverageData >= 16X There is a 1.55% of reference with a coverageData >= 17X There is a 1.49% of reference with a coverageData >= 18X There is a 1.44% of reference with a coverageData >= 19X There is a 1.39% of reference with a coverageData >= 20X There is a 1.34% of reference with a coverageData >= 21X There is a 1.3% of reference with a coverageData >= 22X There is a 1.26% of reference with a coverageData >= 23X There is a 1.22% of reference with a coverageData >= 24X There is a 1.18% of reference with a coverageData >= 25X There is a 1.14% of reference with a coverageData >= 26X There is a 1.11% of reference with a coverageData >= 27X There is a 1.08% of reference with a coverageData >= 28X There is a 1.05% of reference with a coverageData >= 29X There is a 1.02% of reference with a coverageData >= 30X There is a 1% of reference with a coverageData >= 31X There is a 0.97% of reference with a coverageData >= 32X There is a 0.94% of reference with a coverageData >= 33X There is a 0.92% of reference with a coverageData >= 34X There is a 0.9% of reference with a coverageData >= 35X There is a 0.88% of reference with a coverageData >= 36X There is a 0.86% of reference with a coverageData >= 37X There is a 0.84% of reference with a coverageData >= 38X There is a 0.82% of reference with a coverageData >= 39X There is a 0.8% of reference with a coverageData >= 40X There is a 0.78% of reference with a coverageData >= 41X There is a 0.76% of reference with a coverageData >= 42X There is a 0.75% of reference with a coverageData >= 43X There is a 0.73% of reference with a coverageData >= 44X There is a 0.71% of reference with a coverageData >= 45X There is a 0.7% of reference with a coverageData >= 46X There is a 0.68% of reference with a coverageData >= 47X There is a 0.67% of reference with a coverageData >= 48X There is a 0.66% of reference with a coverageData >= 49X There is a 0.64% of reference with a coverageData >= 50X There is a 0.63% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 654085420 2.6242077848223295 22.70421461918665 chr2 243199373 397848708 1.635895286621483 12.56456874301161 chr3 198022430 344980393 1.7421278640000528 13.335848415547085 chr4 191154276 225131559 1.1777479620701763 10.014422181293373 chr5 180915260 355319846 1.9640125769379542 15.882951982020451 chr6 171115067 202600075 1.1839990396637603 11.183395721951294 chr7 159138663 179853436 1.1301680723558674 10.399939924224833 chr8 146364022 259099165 1.7702380780435236 20.050595910518133 chr9 141213431 116794724 0.8270794298596145 8.679291842651036 chr10 135534747 186504359 1.376063062264026 10.8759360213492 chr11 135006516 177216373 1.3126505168091294 9.93541596109831 chr12 133851895 253516573 1.8940080975319775 14.56621179592195 chr13 115169878 57506735 0.49932096828304356 4.848726897390868 chr14 107349540 183492605 1.7093003379427616 13.068902110316358 chr15 102531392 222444950 2.1695301864232954 16.160722342322703 chr16 90354753 240659776 2.663498797899431 22.376136648623763 chr17 81195210 140877989 1.7350529544784723 11.971614718888265 chr18 78077248 81770846 1.0473069696308968 9.411966644186586 chr19 59128983 254368354 4.301923373178937 27.373323873753403 chr20 63025520 99185794 1.5737401928615582 12.553966548017355 chr21 48129895 46474164 0.9655986991037483 8.728593945184763 chr22 51304566 67639789 1.3183970604097888 11.246530245934668 chrMT 16571 102273 6.171806167400881 17.306720453981207 chrX 155270560 249050090 1.6039749582921579 13.440315318226272 chrY 59373566 3629675 0.061132844875781925 2.5037709653920484