BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716107.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 910,679 number of mapped reads = 808,399 (88.77%) number of supplementary alignments = 2,530 (0.28%) number of secondary alignments = 0 number of mapped bases = 46,180,685 bp number of sequenced bases = 46,166,805 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,298 duplication rate = 1.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7219 >>>>>>> ACTG content number of A's = 10,922,758 bp (23.66%) number of C's = 8,806,171 bp (19.07%) number of T's = 14,738,895 bp (31.93%) number of G's = 11,698,630 bp (25.34%) number of N's = 351 bp (0%) GC percentage = 44.41% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 243,020 number of insertions = 3,016 mapped reads with insertion percentage = 0.37% number of deletions = 8,886 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.15% >>>>>>> Coverage mean coverageData = 0.0149X std coverageData = 0.1538X There is a 1.4% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 3942177 0.015816117063957084 0.1941201444168084 chr2 243199373 3320803 0.013654652802085965 0.1968619625883826 chr3 198022430 2702416 0.01364701968357827 0.12370622737394114 chr4 191154276 2870605 0.015017215727886725 0.13269590642625295 chr5 180915260 2681441 0.0148215302567622 0.12668320061649627 chr6 171115067 2499008 0.014604254574496354 0.14203431540390743 chr7 159138663 2657519 0.016699392529142966 0.20425266288426466 chr8 146364022 2401147 0.016405308949490334 0.15301347877250235 chr9 141213431 1568879 0.011109984290375326 0.12268838552003601 chr10 135534747 2076792 0.015322948881883404 0.18495426821685515 chr11 135006516 1621832 0.012012990543360145 0.12948978142548417 chr12 133851895 2337512 0.017463421044580655 0.13842935828848313 chr13 115169878 1437158 0.012478592709805596 0.11636179764491279 chr14 107349540 1566214 0.014589852923449881 0.1281141317494247 chr15 102531392 1675636 0.01634266313286764 0.1348637053027971 chr16 90354753 1610112 0.01781989266242585 0.14657706475851348 chr17 81195210 2079724 0.025613875498320653 0.17345067708323186 chr18 78077248 881055 0.01128440131496438 0.17028246872097624 chr19 59128983 1212259 0.020501942338497517 0.1897207890943383 chr20 63025520 1481693 0.02350941332971152 0.16443083306509376 chr21 48129895 592559 0.012311662013806596 0.11979201551767057 chr22 51304566 416612 0.008120368857617858 0.09482997982468433 chrMT 16571 4595 0.27729165409450246 0.53340777826214 chrX 155270560 2408079 0.01550892197464864 0.13530287026959467 chrY 59373566 134858 0.0022713474882071257 0.06899482077772505