BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818923.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 = 1,508,104 number of mapped reads = 1,489,015 (98.73%) number of supplementary alignments = 22,185 (1.47%) number of secondary alignments = 0 number of mapped bases = 137,819,798 bp number of sequenced bases = 137,733,341 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 393,414 duplication rate = 22.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1805 >>>>>>> ACTG content number of A's = 40,241,562 bp (29.22%) number of C's = 30,354,513 bp (22.04%) number of T's = 38,307,012 bp (27.81%) number of G's = 28,828,117 bp (20.93%) number of N's = 2,137 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 824,643 number of insertions = 17,886 mapped reads with insertion percentage = 1.16% number of deletions = 45,100 mapped reads with deletion percentage = 2.96% homopolymer indels = 42.06% >>>>>>> Coverage mean coverageData = 0.0445X std coverageData = 0.5661X There is a 2.94% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.12% 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 13193529 0.05293278286355804 0.7924648547711678 chr2 243199373 10595934 0.04356891989191107 0.9117728617762509 chr3 198022430 8249201 0.04165791218701841 0.2866895058874777 chr4 191154276 7159385 0.0374534389175788 0.34355821367308514 chr5 180915260 6126321 0.03386293118667823 0.2689792136991929 chr6 171115067 6908527 0.04037357505169314 0.30874053414619995 chr7 159138663 12519780 0.07867214518447978 1.2429971763714298 chr8 146364022 11827758 0.08081055602585176 0.48274226745291654 chr9 141213431 5181134 0.03669009359315121 0.43847780599499403 chr10 135534747 6380537 0.047076761798950345 0.6397353498514163 chr11 135006516 6042791 0.04475925443480076 0.3374074683089191 chr12 133851895 5467626 0.040848327175345554 0.28938077511628857 chr13 115169878 3346876 0.029060341628563677 0.23820326327643174 chr14 107349540 4111142 0.03829678264108072 0.2927094674946473 chr15 102531392 3877695 0.03781958797555387 0.2712905457957657 chr16 90354753 3429387 0.03795469398272828 0.594950914503143 chr17 81195210 3416546 0.04207817185274846 0.35152942967768525 chr18 78077248 2693171 0.03449367221549612 0.4872521352400016 chr19 59128983 2334465 0.03948089213710981 0.6763872449407221 chr20 63025520 5855056 0.09289976504755534 0.46510245861961574 chr21 48129895 1358052 0.028216392327471314 0.2720372349010008 chr22 51304566 1278166 0.024913299139885523 0.24458767202295204 chrMT 16571 180970 10.920885884979784 7.4271765472995 chrX 155270560 5798192 0.03734250716942091 0.30765021647659596 chrY 59373566 487557 0.00821168464093937 0.6663036768800874