BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231824.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,393,981 number of mapped reads = 242,503 (17.4%) number of supplementary alignments = 2,554 (0.18%) number of secondary alignments = 0 number of mapped bases = 14,528,331 bp number of sequenced bases = 14,520,658 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,729 duplication rate = 8.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2915 >>>>>>> ACTG content number of A's = 3,816,790 bp (26.29%) number of C's = 2,876,115 bp (19.81%) number of T's = 4,409,602 bp (30.37%) number of G's = 3,415,721 bp (23.52%) number of N's = 2,430 bp (0.02%) GC percentage = 43.33% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 141,310 number of insertions = 2,230 mapped reads with insertion percentage = 0.9% number of deletions = 4,403 mapped reads with deletion percentage = 1.79% homopolymer indels = 37.58% >>>>>>> Coverage mean coverageData = 0.0047X std coverageData = 0.1163X There is a 0.3% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.04% 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 1153979 0.004629793881235706 0.11438638993395998 chr2 243199373 1168672 0.004805407125782352 0.12025629033728766 chr3 198022430 945476 0.004774590434023055 0.10616948992109708 chr4 191154276 914629 0.004784768717389299 0.10935963164630547 chr5 180915260 862216 0.004765855572382341 0.11297609512746587 chr6 171115067 811706 0.004743626696531639 0.11138455375341175 chr7 159138663 901118 0.00566247059647598 0.12361762504155409 chr8 146364022 710398 0.00485363814339565 0.1112906340027647 chr9 141213431 656318 0.004647702384626573 0.10358677898006781 chr10 135534747 750602 0.005538077995600641 0.12165506033666323 chr11 135006516 656370 0.004861765338792981 0.11835889553644402 chr12 133851895 664697 0.00496591400517714 0.11263219429716688 chr13 115169878 448556 0.0038947336559651473 0.13198214141791 chr14 107349540 472560 0.0044020682342933186 0.12023138312954514 chr15 102531392 411118 0.004009679298999471 0.10068937141161698 chr16 90354753 403470 0.004465398737795233 0.12089547222123002 chr17 81195210 429071 0.005284437345503509 0.11845207668570025 chr18 78077248 322141 0.004125926672005653 0.10726203246801495 chr19 59128983 303365 0.005130563466650526 0.11089110260042608 chr20 63025520 306705 0.0048663620704755784 0.11349918972307245 chr21 48129895 200969 0.004175554507235057 0.09885198735243546 chr22 51304566 170663 0.003326468057443464 0.08647830107183206 chrMT 16571 159950 9.652404803572507 8.016500833560581 chrX 155270560 639688 0.004119827995725654 0.10498978069803322 chrY 59373566 63894 0.0010761354640548286 0.047973432340194196