BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008812.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 = 1,559,480 number of mapped reads = 1,285,557 (82.43%) number of supplementary alignments = 14,079 (0.9%) number of secondary alignments = 0 number of mapped bases = 84,265,056 bp number of sequenced bases = 84,229,882 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,820 duplication rate = 9.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9931 >>>>>>> ACTG content number of A's = 22,453,735 bp (26.66%) number of C's = 15,745,821 bp (18.69%) number of T's = 26,387,532 bp (31.33%) number of G's = 19,604,722 bp (23.28%) number of N's = 38,072 bp (0.05%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 688,026 number of insertions = 5,725 mapped reads with insertion percentage = 0.44% number of deletions = 20,214 mapped reads with deletion percentage = 1.56% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.3167X There is a 1.59% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 7808366 0.031327368287680214 0.39334469876197475 chr2 243199373 6413914 0.026373069637807 0.33430546919317955 chr3 198022430 9181201 0.04636444972420548 0.33901365777542186 chr4 191154276 5011376 0.0262163949709396 0.257340249723008 chr5 180915260 2826044 0.015620816066041085 0.19036706116618754 chr6 171115067 4780007 0.02793446003209057 0.27327798527937963 chr7 159138663 3306538 0.020777716349169025 0.33495793783667066 chr8 146364022 7534284 0.05147633890519898 0.5588423475898049 chr9 141213431 1058840 0.007498153628177195 0.184607913859191 chr10 135534747 6229584 0.04596300312568555 0.3787761344147822 chr11 135006516 4097954 0.030353749740494006 0.4323394175008969 chr12 133851895 3354466 0.025061027339209504 0.24700542302798056 chr13 115169878 2525920 0.021932123606139445 0.2281855226849413 chr14 107349540 3268081 0.03044336286862524 0.2725028565497021 chr15 102531392 2534432 0.024718595452210383 0.24569820905693432 chr16 90354753 1424980 0.015770946770226908 0.1931849479000237 chr17 81195210 2667670 0.03285501694003871 0.32274365115734865 chr18 78077248 1214435 0.015554275171174066 0.354956549399207 chr19 59128983 1715493 0.02901272629701749 0.31362227813917426 chr20 63025520 1268793 0.02013141660711407 0.22046239564909786 chr21 48129895 453703 0.009426635981649244 0.14952371944943338 chr22 51304566 774619 0.015098441725440188 0.18446842324462623 chrMT 16571 31584 1.9059803270774245 2.5000740414929723 chrX 155270560 4539762 0.029237751187346783 0.29732316838382516 chrY 59373566 243010 0.004092898849969699 0.12351304393082244