BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716408.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 = 1,114,125 number of mapped reads = 1,021,024 (91.64%) number of supplementary alignments = 3,385 (0.3%) number of secondary alignments = 0 number of mapped bases = 59,003,178 bp number of sequenced bases = 58,984,259 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,897 duplication rate = 2.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1582 >>>>>>> ACTG content number of A's = 14,859,606 bp (25.19%) number of C's = 11,919,076 bp (20.21%) number of T's = 18,164,235 bp (30.8%) number of G's = 14,040,260 bp (23.8%) number of N's = 1,082 bp (0%) GC percentage = 44.01% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 299,178 number of insertions = 4,523 mapped reads with insertion percentage = 0.44% number of deletions = 11,712 mapped reads with deletion percentage = 1.14% homopolymer indels = 42.11% >>>>>>> Coverage mean coverageData = 0.0191X std coverageData = 0.2015X There is a 1.77% of reference with a coverageData >= 1X There is a 0.09% 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 5001525 0.02006624890214416 0.29397499954284373 chr2 243199373 4684805 0.019263228116957357 0.29705715726415893 chr3 198022430 3432065 0.01733169823236691 0.14047283757422685 chr4 191154276 3618366 0.018929035100423285 0.16479880264923383 chr5 180915260 3354347 0.01854098432603198 0.14368013138757954 chr6 171115067 3132644 0.018307236498349966 0.16196793689167782 chr7 159138663 3387896 0.021288956034524433 0.25659063315924574 chr8 146364022 3113756 0.02127405326426463 0.2469093974954267 chr9 141213431 1994426 0.014123486596682153 0.15090525497153687 chr10 135534747 2657864 0.01961020372141175 0.21517171373047125 chr11 135006516 2126721 0.015752728557190527 0.15850180662057742 chr12 133851895 2967697 0.0221714978334823 0.15806566709987138 chr13 115169878 1768417 0.015354856935769264 0.1317699989124565 chr14 107349540 2007822 0.018703592022844252 0.14697931937029282 chr15 102531392 2160396 0.02107058099825661 0.1556809598348219 chr16 90354753 1966709 0.021766525110195365 0.1635366104840128 chr17 81195210 2552400 0.03143535191300078 0.1919161740489749 chr18 78077248 1086264 0.013912682988006955 0.22594669415952554 chr19 59128983 1468175 0.02483003977930755 0.2467093436274471 chr20 63025520 1745751 0.02769911299422837 0.18069053161205534 chr21 48129895 754385 0.015673938204103708 0.1530679801901885 chr22 51304566 551050 0.010740759409211258 0.11031651751226093 chrMT 16571 71897 4.338724277352 3.2481304186896978 chrX 155270560 3182976 0.020499546082657267 0.1611749172454573 chrY 59373566 214824 0.0036181758057112485 0.1597747988835413