BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819019.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,232,899 number of mapped reads = 1,147,225 (93.05%) number of supplementary alignments = 17,196 (1.39%) number of secondary alignments = 0 number of mapped bases = 106,151,677 bp number of sequenced bases = 106,087,195 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 333,370 duplication rate = 25.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1476 >>>>>>> ACTG content number of A's = 31,490,691 bp (29.68%) number of C's = 21,932,978 bp (20.67%) number of T's = 29,793,608 bp (28.08%) number of G's = 22,864,640 bp (21.55%) number of N's = 5,278 bp (0%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 688,961 number of insertions = 18,510 mapped reads with insertion percentage = 1.57% number of deletions = 34,094 mapped reads with deletion percentage = 2.91% homopolymer indels = 40.91% >>>>>>> Coverage mean coverageData = 0.0343X std coverageData = 0.4501X There is a 2.16% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 10941823 0.04389887959396498 0.8386128397276378 chr2 243199373 8647207 0.035556041503445816 0.6214164953903579 chr3 198022430 5584918 0.028203461597759407 0.2443732105522215 chr4 191154276 5689564 0.029764251781634225 0.3121752017523904 chr5 180915260 5866510 0.03242683895211493 0.27152530497557 chr6 171115067 4273835 0.024976380367486867 0.27855309227924724 chr7 159138663 5270583 0.033119437480758525 0.5030479053586321 chr8 146364022 9506827 0.06495330525967645 0.40752415407894294 chr9 141213431 4403075 0.03118028482715642 0.3787168935224223 chr10 135534747 5793815 0.04274782023240136 0.5923312749247852 chr11 135006516 3548270 0.02628221292667089 0.2871399308448445 chr12 133851895 4824447 0.0360431729412572 0.2824742017369607 chr13 115169878 2261566 0.019636783847248672 0.2026747710859206 chr14 107349540 2507505 0.02335832086471912 0.24362551102704808 chr15 102531392 2770267 0.027018720276420317 0.24019235069956124 chr16 90354753 3449737 0.038179917330967636 0.5211198672463524 chr17 81195210 3756873 0.04626963831979743 0.3515044934104078 chr18 78077248 2479315 0.031754641249650606 0.44911414309598047 chr19 59128983 2288088 0.03869655596816201 0.7281373098629369 chr20 63025520 3158272 0.05011100265416295 0.34943620964483363 chr21 48129895 1477936 0.030707235077076317 0.2838488535898309 chr22 51304566 877007 0.017094131543769417 0.21928815162719467 chrMT 16571 11338 0.6842073501900912 1.2028552799373882 chrX 155270560 6320266 0.040704857379273957 0.3385082785505201 chrY 59373566 442633 0.007455051630215372 0.5179349283456042