BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236110.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 = 1,611,169 number of mapped reads = 1,433,763 (88.99%) number of supplementary alignments = 10,259 (0.64%) number of secondary alignments = 0 number of mapped bases = 94,443,654 bp number of sequenced bases = 94,390,194 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,780 duplication rate = 4.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7756 >>>>>>> ACTG content number of A's = 26,024,644 bp (27.57%) number of C's = 16,719,509 bp (17.71%) number of T's = 30,718,272 bp (32.54%) number of G's = 20,876,142 bp (22.12%) number of N's = 51,627 bp (0.05%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 784,484 number of insertions = 6,712 mapped reads with insertion percentage = 0.46% number of deletions = 30,745 mapped reads with deletion percentage = 2.12% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 0.0305X std coverageData = 0.3018X There is a 2.45% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 9787369 0.039267180000325856 0.5241797643081474 chr2 243199373 4248795 0.017470419218556126 0.2634886190853634 chr3 198022430 5084096 0.025674344062942767 0.19119995027461845 chr4 191154276 5067101 0.026507913430092456 0.2065058684247372 chr5 180915260 4025158 0.02224885838817577 0.17977002618455307 chr6 171115067 10471889 0.061197936473940076 0.39671198779462663 chr7 159138663 5911225 0.037145121672914894 0.30379467069904387 chr8 146364022 6876098 0.04697942777221577 0.5480980186697297 chr9 141213431 3977032 0.028163270107076428 0.26917424871145684 chr10 135534747 2903809 0.02142483063771093 0.25032863838256625 chr11 135006516 3598874 0.0266570392794967 0.22776031709722358 chr12 133851895 3311501 0.024740038234049657 0.19481457639275818 chr13 115169878 4441314 0.03856315624472573 0.2372144901338737 chr14 107349540 2334806 0.021749566882168288 0.1827341586363396 chr15 102531392 2486931 0.024255312948448023 0.18884837062475243 chr16 90354753 2131596 0.023591409740226946 0.19215790943095842 chr17 81195210 2658693 0.032744456230854015 0.23432229671665988 chr18 78077248 1925908 0.02466669931809072 0.38714542407154806 chr19 59128983 2493818 0.04217589874664342 0.37151247966667156 chr20 63025520 1595062 0.0253081926178475 0.19253244276194015 chr21 48129895 1644934 0.03417697046710781 0.23024571017118659 chr22 51304566 1107554 0.02158782514601137 0.1738231507433414 chrMT 16571 40387 2.437209583006457 2.1895606293086294 chrX 155270560 6100678 0.0392906292087824 0.25291524908697427 chrY 59373566 219026 0.0036889480412882728 0.09669942928422032