BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008709.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,907,306 number of mapped reads = 1,402,846 (73.55%) number of supplementary alignments = 5,251 (0.28%) number of secondary alignments = 0 number of mapped bases = 94,553,956 bp number of sequenced bases = 94,510,636 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,871 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0445 >>>>>>> ACTG content number of A's = 28,730,501 bp (30.4%) number of C's = 16,421,502 bp (17.38%) number of T's = 28,308,230 bp (29.95%) number of G's = 21,028,625 bp (22.25%) number of N's = 21,778 bp (0.02%) GC percentage = 39.63% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 861,665 number of insertions = 6,787 mapped reads with insertion percentage = 0.48% number of deletions = 27,589 mapped reads with deletion percentage = 1.94% homopolymer indels = 47.76% >>>>>>> Coverage mean coverageData = 0.0305X std coverageData = 0.2388X There is a 2.79% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% 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 8206149 0.032923284070774696 0.3494804050851715 chr2 243199373 7880489 0.03240341002030462 0.26968279687665114 chr3 198022430 7549256 0.03812323684746218 0.2123031832161672 chr4 191154276 5175178 0.027073304915240296 0.17907308848171422 chr5 180915260 4507773 0.024916488526175184 0.16992897688131522 chr6 171115067 5053426 0.02953232633804246 0.19712264643539043 chr7 159138663 5502061 0.03457400543826361 0.318202463926458 chr8 146364022 7976734 0.05449928125096207 0.3332011933682508 chr9 141213431 2500415 0.017706637267385708 0.18871699237247133 chr10 135534747 5358911 0.03953901946635131 0.2696816793823556 chr11 135006516 4838718 0.03584062564802428 0.2539260626277147 chr12 133851895 4065821 0.030375520645411856 0.18870072188803197 chr13 115169878 3063083 0.02659621641693499 0.17624204880492578 chr14 107349540 3469687 0.03232139606746336 0.19530111829372582 chr15 102531392 2484558 0.024232168817136513 0.16891854556295272 chr16 90354753 2133025 0.0236072251782925 0.17976670405256653 chr17 81195210 2652670 0.03267027697816164 0.2130709014297592 chr18 78077248 1354440 0.017347435196486433 0.331419231145542 chr19 59128983 1327526 0.022451358583319453 0.21538473051749868 chr20 63025520 2112030 0.03351071121666271 0.19913577900096452 chr21 48129895 1021340 0.021220490923572553 0.16082276821563612 chr22 51304566 1049865 0.0204633833175784 0.15328270559561696 chrMT 16571 29961 1.8080381389173859 1.9371396346654064 chrX 155270560 5043014 0.03247888073566554 0.20632076798939908 chrY 59373566 197826 0.003331886786116232 0.07537274509822174