BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716383.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 = 944,689 number of mapped reads = 828,123 (87.66%) number of supplementary alignments = 3,117 (0.33%) number of secondary alignments = 0 number of mapped bases = 47,393,876 bp number of sequenced bases = 47,379,521 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,590 duplication rate = 1.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4704 >>>>>>> ACTG content number of A's = 12,057,905 bp (25.45%) number of C's = 9,570,326 bp (20.2%) number of T's = 14,566,886 bp (30.75%) number of G's = 11,184,057 bp (23.61%) number of N's = 347 bp (0%) GC percentage = 43.8% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 248,885 number of insertions = 3,633 mapped reads with insertion percentage = 0.44% number of deletions = 9,096 mapped reads with deletion percentage = 1.09% homopolymer indels = 39.35% >>>>>>> Coverage mean coverageData = 0.0153X std coverageData = 0.1559X There is a 1.44% of reference with a coverageData >= 1X There is a 0.07% 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 3972786 0.015938921171233512 0.1894609730012961 chr2 243199373 3716552 0.01528191439868556 0.20477901139407403 chr3 198022430 2747802 0.013876215941800128 0.1244942169012334 chr4 191154276 2902858 0.015185943316277163 0.13569179571549236 chr5 180915260 2715980 0.015012442842024493 0.1279140001416156 chr6 171115067 2520055 0.014727253678952772 0.1387088192146167 chr7 159138663 2709909 0.017028602282526402 0.2099430222345578 chr8 146364022 2454038 0.016766675078114485 0.15855986678004377 chr9 141213431 1568861 0.011109856823746461 0.12350507263697595 chr10 135534747 2102009 0.015509004491667366 0.185860842496339 chr11 135006516 1687840 0.012501915092750043 0.13515412310889113 chr12 133851895 2363749 0.017659436199988054 0.13921822709989962 chr13 115169878 1439522 0.012499118910241443 0.11746504696284711 chr14 107349540 1580727 0.014725046795729167 0.13015088407907016 chr15 102531392 1734413 0.01691592171107947 0.1370934609863612 chr16 90354753 1615791 0.01788274491769127 0.14563583936025656 chr17 81195210 2086378 0.025695826145409318 0.1735261671775429 chr18 78077248 888982 0.01138592897126702 0.17610553696008438 chr19 59128983 1240193 0.020974367172863433 0.1877205576351985 chr20 63025520 1541531 0.024458838261072657 0.16820738416192943 chr21 48129895 591884 0.012297637466277456 0.12099683518914905 chr22 51304566 423688 0.008258290304999364 0.09522795911161298 chrMT 16571 12906 0.7788304869953533 0.979485637362183 chrX 155270560 2632665 0.016955339119019086 0.14165084550862733 chrY 59373566 142757 0.002404386490782784 0.07744616700840666