BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708627.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,301,249 number of mapped reads = 2,435,209 (73.77%) number of supplementary alignments = 818 (0.02%) number of secondary alignments = 0 number of mapped bases = 118,579,367 bp number of sequenced bases = 118,557,587 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,359 duplication rate = 2.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7916 >>>>>>> ACTG content number of A's = 34,885,332 bp (29.42%) number of C's = 22,374,947 bp (18.87%) number of T's = 37,367,325 bp (31.52%) number of G's = 23,919,711 bp (20.18%) number of N's = 10,272 bp (0.01%) GC percentage = 39.05% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 751,995 number of insertions = 5,441 mapped reads with insertion percentage = 0.22% number of deletions = 14,125 mapped reads with deletion percentage = 0.58% homopolymer indels = 48.23% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 0.4223X There is a 3.24% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.01% 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 9435810 0.03785671611225394 0.7874242120908642 chr2 243199373 10236937 0.042092777105967295 0.3941476236274503 chr3 198022430 7860708 0.03969604857389135 0.23104236076619772 chr4 191154276 8064368 0.0421877457766103 0.23932681673185335 chr5 180915260 6780164 0.03747701548227607 0.2288264074339574 chr6 171115067 6582420 0.03846779898113823 0.283219952975625 chr7 159138663 6678788 0.04196835560947248 0.6339148662499745 chr8 146364022 6764493 0.04621691114774094 0.7515952845656056 chr9 141213431 5135869 0.03636955042895318 0.3397271711552111 chr10 135534747 5355706 0.03951537239376704 0.3120089345715281 chr11 135006516 5451752 0.040381399072619575 0.3936070781403013 chr12 133851895 5368480 0.040107612970290786 0.23898668563613581 chr13 115169878 4067822 0.03532019023238003 0.21641053028610552 chr14 107349540 3938789 0.03669125177434389 0.2433324571109015 chr15 102531392 3453870 0.03368597590092213 0.2105425197515094 chr16 90354753 3120104 0.03453170858648687 0.23789125041529444 chr17 81195210 2973116 0.036616889099738766 0.2921723635206017 chr18 78077248 3141435 0.04023496063795691 0.739377765568337 chr19 59128983 2084888 0.03526000100492173 0.5581883318089442 chr20 63025520 2462825 0.03907663118051227 0.24102150664429103 chr21 48129895 1609704 0.033444992971623975 0.22878317963261316 chr22 51304566 1202425 0.02343699779080092 0.17137204497335426 chrMT 16571 15270 0.9214893488624706 1.204775553765326 chrX 155270560 6524904 0.04202280200444952 0.28530579194969735 chrY 59373566 268720 0.00452591983442598 0.09066289056336768