BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716189.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 = 497,856 number of mapped reads = 441,512 (88.68%) number of supplementary alignments = 1,703 (0.34%) number of secondary alignments = 0 number of mapped bases = 25,531,529 bp number of sequenced bases = 25,523,300 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,205 duplication rate = 0.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9985 >>>>>>> ACTG content number of A's = 6,094,072 bp (23.88%) number of C's = 4,867,353 bp (19.07%) number of T's = 8,033,573 bp (31.48%) number of G's = 6,528,131 bp (25.58%) number of N's = 171 bp (0%) GC percentage = 44.65% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 135,619 number of insertions = 1,913 mapped reads with insertion percentage = 0.43% number of deletions = 4,976 mapped reads with deletion percentage = 1.12% homopolymer indels = 39.13% >>>>>>> Coverage mean coverageData = 0.0082X std coverageData = 0.1033X There is a 0.79% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 2202054 0.008834698149056968 0.11416738627930272 chr2 243199373 1958243 0.008052006778816819 0.13282590803894137 chr3 198022430 1421407 0.00717801008703913 0.08749787859676304 chr4 191154276 1492161 0.007806056088434036 0.09344864357871596 chr5 180915260 1389290 0.007679230596689301 0.08956127136732199 chr6 171115067 1333829 0.00779492433591485 0.09593924326348234 chr7 159138663 1417870 0.008909651327157373 0.12145854011954249 chr8 146364022 1286851 0.008792126524098935 0.10174959278194616 chr9 141213431 835771 0.005918495104052815 0.08289598757281647 chr10 135534747 1124582 0.008297370415278083 0.11910291301581451 chr11 135006516 924657 0.006848980533650687 0.09018086041620052 chr12 133851895 1280225 0.00956448916916716 0.10021536180249423 chr13 115169878 711401 0.006176971030567559 0.08031992795414426 chr14 107349540 863599 0.008044738710571092 0.09285906102523048 chr15 102531392 972991 0.009489688777462419 0.09993796731812477 chr16 90354753 968546 0.010719369682743752 0.10896248820527642 chr17 81195210 1278780 0.015749451229943243 0.13105546012167002 chr18 78077248 449982 0.005763292271776792 0.09736612876235773 chr19 59128983 784943 0.01327509725645036 0.13036883591371762 chr20 63025520 884627 0.01403601271358015 0.12393273983816265 chr21 48129895 325295 0.006758689168135522 0.08704069761952064 chr22 51304566 271834 0.005298436790206938 0.07439269504666149 chrMT 16571 1122 0.0677086476374389 0.2668531481930629 chrX 155270560 1271421 0.00818842284074972 0.09412534923406417 chrY 59373566 80048 0.0013482094034911092 0.055063994185499704