BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524885.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 = 2,745,952 number of mapped reads = 2,529,434 (92.12%) number of supplementary alignments = 9,389 (0.34%) number of secondary alignments = 0 number of mapped bases = 147,523,175 bp number of sequenced bases = 147,478,996 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,075 duplication rate = 4.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1817 >>>>>>> ACTG content number of A's = 38,103,291 bp (25.84%) number of C's = 27,115,319 bp (18.39%) number of T's = 47,774,100 bp (32.39%) number of G's = 34,466,306 bp (23.37%) number of N's = 19,980 bp (0.01%) GC percentage = 41.76% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 730,073 number of insertions = 10,476 mapped reads with insertion percentage = 0.41% number of deletions = 27,949 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.06% >>>>>>> Coverage mean coverageData = 0.0477X std coverageData = 0.448X There is a 4.11% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11932732 0.0478744323770411 0.9261586825063741 chr2 243199373 12528216 0.05151417886262396 0.475882138679774 chr3 198022430 9656448 0.048764415223063365 0.2500404230092812 chr4 191154276 9587944 0.05015814555987228 0.29341382731804044 chr5 180915260 8848959 0.04891217578881958 0.25119553472156025 chr6 171115067 8497749 0.049661021375750625 0.2866163828799527 chr7 159138663 8136605 0.05112902701714919 0.637474604302569 chr8 146364022 7701854 0.05262122408743318 0.42969180464107876 chr9 141213431 6184959 0.04379865963316195 0.38782194063071046 chr10 135534747 6991029 0.051581082746256945 0.41876544474668903 chr11 135006516 6685752 0.04952169864156779 0.4066242764983909 chr12 133851895 6593682 0.049261028392612594 0.2640158200944583 chr13 115169878 4743432 0.04118639424103584 0.22808969531571024 chr14 107349540 4588868 0.042746974043857106 0.25568283636873584 chr15 102531392 4129141 0.04027196860840434 0.2282266507529526 chr16 90354753 4203404 0.04652111660357259 0.2789471696049956 chr17 81195210 3894508 0.04796475062999406 0.2810760253376807 chr18 78077248 4060589 0.052007327409900515 0.8025855018495711 chr19 59128983 2947057 0.04984115826920277 0.5808083970114047 chr20 63025520 3088618 0.049005831288658944 0.26070986789928746 chr21 48129895 1957913 0.040679768779882025 0.2679395227394866 chr22 51304566 1713525 0.03339907407071722 0.20544732068974247 chrMT 16571 32964 1.989258342888178 1.8446859162732352 chrX 155270560 8382891 0.05398892745669237 0.3166315346812965 chrY 59373566 434336 0.00731530930784922 0.18768808724342034