BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716716.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 = 1,789,173 number of mapped reads = 1,512,380 (84.53%) number of supplementary alignments = 6,337 (0.35%) number of secondary alignments = 0 number of mapped bases = 85,559,863 bp number of sequenced bases = 85,537,406 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,797 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9362 >>>>>>> ACTG content number of A's = 21,591,801 bp (25.24%) number of C's = 15,094,298 bp (17.65%) number of T's = 26,863,106 bp (31.41%) number of G's = 21,986,433 bp (25.7%) number of N's = 1,768 bp (0%) GC percentage = 43.35% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 421,259 number of insertions = 5,416 mapped reads with insertion percentage = 0.36% number of deletions = 13,345 mapped reads with deletion percentage = 0.88% homopolymer indels = 40.83% >>>>>>> Coverage mean coverageData = 0.0276X std coverageData = 0.2216X There is a 2.49% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 9541264 0.038279800313917776 0.30873235863486226 chr2 243199373 7150890 0.029403406397762382 0.2503647574479588 chr3 198022430 5588194 0.028220005178201276 0.18273141943418264 chr4 191154276 5425755 0.02838416756107512 0.19755475810379264 chr5 180915260 4319949 0.023878300813320003 0.1693655974405677 chr6 171115067 4438069 0.02593616726924462 0.18619865262268837 chr7 159138663 3694648 0.02321653286731459 0.20270043724693754 chr8 146364022 5382374 0.03677388695973386 0.2310768899470817 chr9 141213431 3116000 0.02206588975237065 0.22981213878116716 chr10 135534747 4045961 0.029851835706750537 0.24296299759913936 chr11 135006516 3413881 0.02528678689849311 0.22154052971541868 chr12 133851895 3798482 0.02837824597104135 0.18656265117547724 chr13 115169878 2602148 0.02259399805911056 0.16197310831530803 chr14 107349540 2336073 0.02176136944788026 0.17416037837918494 chr15 102531392 2454158 0.023935674256719348 0.16873952984698948 chr16 90354753 2515997 0.027845762579861183 0.19693235108465518 chr17 81195210 1970560 0.02426941195176415 0.17592542938107672 chr18 78077248 2136476 0.027363618143918186 0.42047539353314467 chr19 59128983 1651713 0.027934067460622485 0.2367306855820282 chr20 63025520 2782446 0.04414792610993134 0.237574320556536 chr21 48129895 1161384 0.02413020015938119 0.18455038959392783 chr22 51304566 1029058 0.020057824872741346 0.15370062156466086 chrMT 16571 18907 1.1409691629955947 1.2770409137048433 chrX 155270560 4738970 0.03052072459840423 0.21527994438991455 chrY 59373566 246506 0.0041517802720490125 0.10157760028135865