BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525087.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 = 1,236,243 number of mapped reads = 1,128,190 (91.26%) number of supplementary alignments = 4,282 (0.35%) number of secondary alignments = 0 number of mapped bases = 65,812,259 bp number of sequenced bases = 65,791,232 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,506 duplication rate = 3.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9096 >>>>>>> ACTG content number of A's = 16,359,628 bp (24.87%) number of C's = 11,705,126 bp (17.79%) number of T's = 20,599,306 bp (31.31%) number of G's = 17,120,206 bp (26.02%) number of N's = 6,966 bp (0.01%) GC percentage = 43.81% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 313,566 number of insertions = 3,969 mapped reads with insertion percentage = 0.35% number of deletions = 12,773 mapped reads with deletion percentage = 1.12% homopolymer indels = 44.23% >>>>>>> Coverage mean coverageData = 0.0213X std coverageData = 0.2089X There is a 1.91% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5266016 0.021127393700656017 0.35053072007531666 chr2 243199373 5565710 0.022885379725053813 0.25106595046735836 chr3 198022430 4318554 0.02180840826970965 0.16107389615102385 chr4 191154276 4274409 0.022361043077058867 0.18436216093008373 chr5 180915260 3974502 0.021968859896064046 0.16093933478595648 chr6 171115067 3777958 0.02207846489637292 0.17074943399335568 chr7 159138663 3575766 0.022469498816890275 0.2434757597482569 chr8 146364022 3342701 0.022838269639788935 0.2058141237973373 chr9 141213431 2755708 0.01951448938309558 0.17685008422641874 chr10 135534747 3193789 0.023564355788409003 0.24373659773681464 chr11 135006516 2976786 0.022049202425162947 0.1814664398156046 chr12 133851895 2947560 0.02202105543593537 0.16332177250846447 chr13 115169878 2049015 0.017791240518636304 0.1454736518802353 chr14 107349540 2006683 0.01869298182367619 0.15168004313630387 chr15 102531392 1946989 0.018989198937238657 0.15275982177028324 chr16 90354753 1956834 0.021657233681995677 0.16957544649379316 chr17 81195210 1750906 0.021564153846021214 0.16374860649770448 chr18 78077248 1772658 0.022703899604658198 0.27179900874037616 chr19 59128983 1314009 0.02222275664710824 0.24754873492991217 chr20 63025520 1407167 0.022326939944327315 0.1664978377984402 chr21 48129895 880197 0.01828794764667573 0.1662452803057157 chr22 51304566 807916 0.015747448287546182 0.13815102782249805 chrMT 16571 4517 0.2725846358095468 0.5939436051494271 chrX 155270560 3716408 0.023935046025466773 0.18282860516504876 chrY 59373566 229501 0.0038653733548697413 0.1312143729638531