BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013317.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 = 1,454,608 number of mapped reads = 1,138,690 (78.28%) number of supplementary alignments = 14,813 (1.02%) number of secondary alignments = 0 number of mapped bases = 70,130,680 bp number of sequenced bases = 70,083,187 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 393,952 duplication rate = 18.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.7941 >>>>>>> ACTG content number of A's = 19,014,425 bp (27.13%) number of C's = 12,234,579 bp (17.46%) number of T's = 23,036,835 bp (32.87%) number of G's = 15,789,670 bp (22.53%) number of N's = 7,678 bp (0.01%) GC percentage = 39.99% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 605,263 number of insertions = 4,642 mapped reads with insertion percentage = 0.4% number of deletions = 28,081 mapped reads with deletion percentage = 2.43% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.0227X std coverageData = 0.4966X There is a 0.63% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 7521643 0.030177028124636046 0.7641555070671907 chr2 243199373 18531473 0.07619868740368833 0.8668262496740217 chr3 198022430 2812522 0.01420304760425372 0.323136267164879 chr4 191154276 4588301 0.02400313033018419 0.4302812750969152 chr5 180915260 1080116 0.0059702868624791515 0.1721100064880719 chr6 171115067 3483269 0.02035629626934021 0.4164192456525805 chr7 159138663 3120397 0.01960803830556249 0.7501957217170827 chr8 146364022 2474759 0.016908246754793334 0.39545015686047685 chr9 141213431 4107252 0.029085420352119338 0.4945291440066455 chr10 135534747 1344989 0.009923573325443991 0.30042984581017773 chr11 135006516 2268018 0.016799322486034673 0.3559320267828658 chr12 133851895 2792240 0.02086066842759305 0.4025563093155712 chr13 115169878 4173691 0.03623943232795645 0.564320610740209 chr14 107349540 623452 0.005807682082289314 0.1904754805673891 chr15 102531392 726149 0.007082211465538281 0.2302730576716707 chr16 90354753 952725 0.010544270980409852 0.25691652076811705 chr17 81195210 1097211 0.013513247887406167 0.3140213609437426 chr18 78077248 3783366 0.048456702777229035 0.7294627835779856 chr19 59128983 630681 0.010666190554977074 0.4916891189619642 chr20 63025520 449652 0.00713444331756406 0.1972188798794378 chr21 48129895 2131242 0.04428104403718313 0.6103553931081642 chr22 51304566 165936 0.00323433200857795 0.11912401664402146 chrMT 16571 5182 0.31271498400820713 0.980330080808853 chrX 155270560 1186462 0.0076412553674051285 0.2233401864894189 chrY 59373566 79952 0.001346592522335613 0.060583782684996756