BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081916.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,403,868 number of mapped reads = 2,244,151 (93.36%) number of supplementary alignments = 16,430 (0.68%) number of secondary alignments = 0 number of mapped bases = 153,039,337 bp number of sequenced bases = 152,984,394 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,715 duplication rate = 2.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4026 >>>>>>> ACTG content number of A's = 42,704,725 bp (27.91%) number of C's = 29,081,381 bp (19.01%) number of T's = 47,431,918 bp (31%) number of G's = 33,764,615 bp (22.07%) number of N's = 1,755 bp (0%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,274,695 number of insertions = 11,500 mapped reads with insertion percentage = 0.51% number of deletions = 33,553 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.0494X std coverageData = 0.3596X There is a 4.22% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 11921797 0.047830560871501296 0.587324855432155 chr2 243199373 13131640 0.05399536946996981 0.4335083935193445 chr3 198022430 10709141 0.05408044432138319 0.2637339104416702 chr4 191154276 10147227 0.05308396553995998 0.274100680435755 chr5 180915260 9502859 0.052526575149050445 0.26005615901562396 chr6 171115067 8921795 0.05213915499328881 0.2908287224485221 chr7 159138663 8358594 0.052523967729953845 0.44856883947686366 chr8 146364022 7795142 0.053258593836673876 0.4295706100924663 chr9 141213431 6426605 0.04550987079975417 0.3476061865666641 chr10 135534747 7137302 0.05266031152882146 0.36442889949355806 chr11 135006516 7030313 0.052073879160025136 0.32792210540085953 chr12 133851895 6977235 0.05212653134272025 0.2610403849566755 chr13 115169878 4957279 0.043043190512019124 0.23517206264017707 chr14 107349540 4701854 0.04379947971831086 0.2506687333154741 chr15 102531392 4308538 0.0420216473799556 0.2385157423673277 chr16 90354753 4123951 0.0456417716066359 0.26668186990344717 chr17 81195210 3848716 0.047400776474375766 0.2680836246829207 chr18 78077248 4259242 0.05455164095947644 0.6108134977246314 chr19 59128983 2783405 0.047073446198119116 0.4494982466473431 chr20 63025520 3130647 0.04967268814283484 0.2567174177054783 chr21 48129895 2016127 0.04188928731300993 0.24596828492648426 chr22 51304566 1602734 0.03123959766076181 0.1979849878652781 chrMT 16571 30803 1.8588497978395992 1.6987642474023594 chrX 155270560 8838158 0.05692101580621594 0.2926503039070719 chrY 59373566 378233 0.0063703938550701165 0.1347017933600314