BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716126.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 = 800,732 number of mapped reads = 712,269 (88.95%) number of supplementary alignments = 14,276 (1.78%) number of secondary alignments = 0 number of mapped bases = 55,653,320 bp number of sequenced bases = 55,627,503 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,090 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9002 >>>>>>> ACTG content number of A's = 14,620,024 bp (26.28%) number of C's = 10,793,130 bp (19.4%) number of T's = 17,171,367 bp (30.87%) number of G's = 13,039,056 bp (23.44%) number of N's = 3,926 bp (0.01%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 386,574 number of insertions = 5,036 mapped reads with insertion percentage = 0.7% number of deletions = 13,487 mapped reads with deletion percentage = 1.86% homopolymer indels = 42.89% >>>>>>> Coverage mean coverageData = 0.018X std coverageData = 0.2004X There is a 1.66% 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 5307121 0.02129230803400887 0.3912143892654079 chr2 243199373 4564897 0.01877018408267031 0.20687261355408748 chr3 198022430 3486115 0.017604647109925882 0.13926317555420134 chr4 191154276 3527887 0.018455705380087863 0.16331562296146754 chr5 180915260 3356406 0.01855236534496869 0.14360094598986523 chr6 171115067 3119837 0.0182323921247683 0.14972539464211712 chr7 159138663 2880661 0.018101578495729853 0.21955425036619572 chr8 146364022 2702670 0.018465398552657976 0.20531371254506176 chr9 141213431 2308180 0.016345329078506703 0.17381930751174615 chr10 135534747 2592171 0.019125508826161014 0.1971089981057229 chr11 135006516 3076027 0.022784285463673472 0.21234456632668347 chr12 133851895 2489977 0.01860247850805549 0.14340977993381823 chr13 115169878 1975148 0.017149866217623325 0.1379546079690939 chr14 107349540 1563219 0.01456195340939514 0.1317589344167512 chr15 102531392 1504070 0.014669360969955426 0.12706338753791022 chr16 90354753 1283074 0.014200404045152997 0.13181730410986262 chr17 81195210 1768171 0.02177678954214171 0.16897345597691574 chr18 78077248 1442489 0.01847515168567417 0.2705894660613464 chr19 59128983 1089687 0.018428982619234292 0.2700390967554182 chr20 63025520 1187247 0.018837559769439426 0.14884529814108013 chr21 48129895 653645 0.013580852399532557 0.13249688614128804 chr22 51304566 599418 0.011683521501770428 0.11380576070024352 chrMT 16571 10194 0.6151710820107417 0.9131356348956505 chrX 155270560 2992580 0.0192733252201834 0.15882654015464437 chrY 59373566 172429 0.0029041375079273493 0.10106690871906975