BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716789.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 = 547,360 number of mapped reads = 460,263 (84.09%) number of supplementary alignments = 1,802 (0.33%) number of secondary alignments = 0 number of mapped bases = 26,811,037 bp number of sequenced bases = 26,803,109 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,010 duplication rate = 1.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4236 >>>>>>> ACTG content number of A's = 6,924,403 bp (25.83%) number of C's = 5,266,980 bp (19.65%) number of T's = 8,349,021 bp (31.15%) number of G's = 6,261,909 bp (23.36%) number of N's = 796 bp (0%) GC percentage = 43.01% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 134,796 number of insertions = 2,194 mapped reads with insertion percentage = 0.47% number of deletions = 4,956 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.78% >>>>>>> Coverage mean coverageData = 0.0087X std coverageData = 0.1124X There is a 0.82% of reference with a coverageData >= 1X There is a 0.04% 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 2123292 0.008518702948387037 0.15859639675554105 chr2 243199373 2269587 0.00933220744775522 0.13441232500941147 chr3 198022430 1750670 0.008840766169771778 0.0978802113714094 chr4 191154276 1716055 0.008977329913352292 0.10234268094270411 chr5 180915260 1582117 0.008745072140404297 0.09751357776452689 chr6 171115067 1542224 0.009012789037449285 0.10582278018446815 chr7 159138663 1469876 0.009236448090556095 0.12126439341967714 chr8 146364022 1349335 0.009219034716058842 0.11836149722890664 chr9 141213431 1100512 0.007793253036957937 0.09989562927501094 chr10 135534747 1328454 0.009801575089818111 0.11835486915798257 chr11 135006516 1245198 0.009223243713658976 0.1095906546714556 chr12 133851895 1217923 0.009099034421589623 0.09937960861083131 chr13 115169878 842999 0.0073196135538148265 0.0889595958234998 chr14 107349540 803175 0.007481867178937143 0.09130511308520017 chr15 102531392 756150 0.00737481453484997 0.08967237185649922 chr16 90354753 778743 0.008618727561570557 0.09936825047603244 chr17 81195210 753159 0.009275904329824383 0.10221222886774452 chr18 78077248 723734 0.009269460931819727 0.1380343549402707 chr19 59128983 552718 0.009347666270532675 0.1299356602937825 chr20 63025520 580620 0.009212458699269756 0.10018799620433151 chr21 48129895 351741 0.007308160551773487 0.09224303675376529 chr22 51304566 332233 0.006475700427911231 0.08390739366487036 chrMT 16571 1909 0.115201255204876 0.36312771112289605 chrX 155270560 1548562 0.009973313679038705 0.10771898839970666 chrY 59373566 90051 0.0015166850513913886 0.056009789769828636