BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238663.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 = 2,541,919 number of mapped reads = 2,320,952 (91.31%) number of supplementary alignments = 17,546 (0.69%) number of secondary alignments = 0 number of mapped bases = 143,339,000 bp number of sequenced bases = 143,269,082 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 336,355 duplication rate = 12.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4615 >>>>>>> ACTG content number of A's = 35,561,151 bp (24.82%) number of C's = 24,785,958 bp (17.3%) number of T's = 48,489,312 bp (33.84%) number of G's = 34,425,300 bp (24.03%) number of N's = 7,361 bp (0.01%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 823,400 number of insertions = 9,095 mapped reads with insertion percentage = 0.39% number of deletions = 40,322 mapped reads with deletion percentage = 1.72% homopolymer indels = 42.67% >>>>>>> Coverage mean coverageData = 0.0463X std coverageData = 0.5231X There is a 3.37% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 12173166 0.0488390598633654 0.6045618331898486 chr2 243199373 13577268 0.055827726167698634 1.170732258174152 chr3 198022430 8212757 0.041473872429502054 0.2723649272841271 chr4 191154276 8299576 0.043418207395998824 0.27862269780444565 chr5 180915260 7932036 0.043843930025582144 0.28117120760874953 chr6 171115067 11746499 0.06864678374581708 0.5541293674507706 chr7 159138663 7208103 0.04529448007238819 0.5364145890907532 chr8 146364022 9175838 0.06269189569004875 0.5907464488172848 chr9 141213431 4343085 0.030755466879067616 0.3592697953690779 chr10 135534747 7818623 0.05768722171296782 0.39475034958805083 chr11 135006516 4756966 0.03523508450510641 0.300054943001369 chr12 133851895 6149625 0.04594350345208038 0.2971270857798366 chr13 115169878 3582867 0.03110941039635381 0.308244757048539 chr14 107349540 1557524 0.014508902413554823 0.19906681707127952 chr15 102531392 3582080 0.034936422203260445 0.339433890788996 chr16 90354753 4452704 0.0492802409630847 0.32627784664711174 chr17 81195210 3120594 0.03843322777291912 0.2670129881821076 chr18 78077248 6975962 0.08934692472767483 0.9996383534981206 chr19 59128983 2681323 0.045347017045769246 0.46328686863891355 chr20 63025520 3219263 0.05107872176223219 0.3070085985775162 chr21 48129895 2422900 0.05034085364200358 0.31005155554194147 chr22 51304566 1485554 0.02895559042444682 0.22434248987121694 chrMT 16571 18480 1.115201255204876 1.485387266824568 chrX 155270560 8511174 0.054815117559954704 0.3299695142538417 chrY 59373566 335033 0.005642797335096901 0.18752788742428425