BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008803.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 = 1,677,474 number of mapped reads = 1,451,083 (86.5%) number of supplementary alignments = 15,446 (0.92%) number of secondary alignments = 0 number of mapped bases = 94,735,145 bp number of sequenced bases = 94,679,886 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,644 duplication rate = 6.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1259 >>>>>>> ACTG content number of A's = 25,528,452 bp (26.96%) number of C's = 18,623,124 bp (19.67%) number of T's = 28,812,628 bp (30.43%) number of G's = 21,566,755 bp (22.78%) number of N's = 148,927 bp (0.16%) GC percentage = 42.45% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 865,427 number of insertions = 7,382 mapped reads with insertion percentage = 0.5% number of deletions = 31,364 mapped reads with deletion percentage = 2.14% homopolymer indels = 44.31% >>>>>>> Coverage mean coverageData = 0.0306X std coverageData = 0.3816X There is a 1.99% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 8259472 0.03313721733916964 0.6490489016140201 chr2 243199373 10697264 0.04398557392662357 0.49351662760341947 chr3 198022430 7113017 0.0359202591342809 0.28202815559440525 chr4 191154276 2587561 0.013536505979076293 0.16824630736516424 chr5 180915260 4677850 0.025856580589166442 0.23053621849972886 chr6 171115067 3815475 0.022297715022371465 0.24099346740741384 chr7 159138663 3958367 0.024873697726114488 0.45255783008096706 chr8 146364022 7219640 0.049326602954379045 0.4149947099480783 chr9 141213431 3145498 0.022274779231162507 0.2720331528635068 chr10 135534747 7733472 0.057058962156767076 0.6154623050006389 chr11 135006516 3156973 0.023383856524376943 0.2627736627440198 chr12 133851895 5137790 0.038384140919334765 0.28256948438242085 chr13 115169878 2528782 0.02195697385387523 0.21450883329739118 chr14 107349540 2587893 0.024107164315748348 0.22743846387794064 chr15 102531392 2043519 0.019930666697668555 0.20299013568240978 chr16 90354753 2232794 0.024711417228930947 0.3674698278762168 chr17 81195210 3223521 0.039700876443327135 0.34144161313554733 chr18 78077248 1394199 0.017856661648730243 0.4976794653033929 chr19 59128983 2858475 0.04834304354600518 0.5349918294859332 chr20 63025520 2496442 0.03961001829100339 0.292396326533244 chr21 48129895 1217517 0.025296481531904443 0.2373122985493781 chr22 51304566 1660384 0.032363279322935895 0.2586863360406848 chrMT 16571 320405 19.335284533220687 12.353434413813714 chrX 155270560 4417470 0.028450145346291016 0.2584413222354745 chrY 59373566 251365 0.004233618038033963 0.19065273170120853