BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238608.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 = 2,046,978 number of mapped reads = 1,821,101 (88.97%) number of supplementary alignments = 16,285 (0.8%) number of secondary alignments = 0 number of mapped bases = 111,373,786 bp number of sequenced bases = 111,326,093 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 338,191 duplication rate = 14.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1828 >>>>>>> ACTG content number of A's = 27,340,950 bp (24.56%) number of C's = 19,880,569 bp (17.86%) number of T's = 37,112,056 bp (33.34%) number of G's = 26,987,063 bp (24.24%) number of N's = 5,455 bp (0%) GC percentage = 42.1% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 656,036 number of insertions = 7,618 mapped reads with insertion percentage = 0.41% number of deletions = 28,466 mapped reads with deletion percentage = 1.55% homopolymer indels = 41.45% >>>>>>> Coverage mean coverageData = 0.036X std coverageData = 0.5564X There is a 2.3% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.28% 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% 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 8762758 0.03515641391320746 0.7490290644554563 chr2 243199373 9300577 0.0382426027060522 1.3723120112136582 chr3 198022430 8669184 0.04377879818967983 0.3148863666145574 chr4 191154276 6694325 0.03502053493169047 0.30072602736350357 chr5 180915260 5766421 0.03187360203887721 0.270364163894666 chr6 171115067 6541750 0.0382301226577552 0.46377352744745315 chr7 159138663 5949679 0.037386759998103036 0.4082442624202586 chr8 146364022 5573570 0.0380801915924393 0.35223196502296006 chr9 141213431 5962108 0.042220544871542705 0.37256124543124924 chr10 135534747 5259768 0.03880752439077486 0.4230543983882216 chr11 135006516 4817832 0.03568592200394239 0.3154570898784213 chr12 133851895 4171744 0.03116686543735522 0.27027021154515096 chr13 115169878 3321133 0.028836819641330176 0.3358909146938708 chr14 107349540 3238232 0.03016530857980388 0.28165683820404364 chr15 102531392 3188097 0.031093862453364526 0.3394169210814216 chr16 90354753 2565406 0.02839259601539722 0.2800349577659509 chr17 81195210 2699703 0.0332495352866259 0.27852856973405227 chr18 78077248 3354418 0.042962810369545815 0.9312936111815546 chr19 59128983 3245984 0.054896665481291976 0.5165868631967331 chr20 63025520 2330521 0.03697741803637638 0.29409047900269614 chr21 48129895 1814020 0.037690088457496114 0.30814387881790084 chr22 51304566 1301801 0.025373979384213093 0.23250194881364133 chrMT 16571 28394 1.7134753485003922 2.0810949844008895 chrX 155270560 6455638 0.04157670327201757 0.3163461509982149 chrY 59373566 360723 0.006075481469312455 0.22239441146287514