BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053619.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 6,285,180 number of mapped reads = 5,116,034 (81.4%) number of supplementary alignments = 180 (0%) number of secondary alignments = 0 number of mapped bases = 241,297,855 bp number of sequenced bases = 241,249,446 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 873,396 duplication rate = 13.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6758 >>>>>>> ACTG content number of A's = 69,799,628 bp (28.93%) number of C's = 47,560,048 bp (19.71%) number of T's = 71,116,234 bp (29.48%) number of G's = 52,764,191 bp (21.87%) number of N's = 9,345 bp (0%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,200,396 number of insertions = 9,545 mapped reads with insertion percentage = 0.19% number of deletions = 31,971 mapped reads with deletion percentage = 0.62% homopolymer indels = 46.44% >>>>>>> Coverage mean coverageData = 0.0779X std coverageData = 0.5692X There is a 4.19% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.17% 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 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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% 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 19368081 0.07770524672032814 0.6119296013950055 chr2 243199373 20250283 0.08326618095351751 0.653642948893866 chr3 198022430 16211027 0.08186459988396264 0.5423223885934219 chr4 191154276 15426600 0.08070235373651803 0.5662132560123245 chr5 180915260 14795165 0.08177953037239645 0.5459020312013797 chr6 171115067 14132735 0.08259199641373485 0.5717592010117392 chr7 159138663 12980370 0.08156641356224037 0.5767826540850044 chr8 146364022 12049707 0.0823269737695511 0.572450377360612 chr9 141213431 9993271 0.07076714253901245 0.5264420940239172 chr10 135534747 11258787 0.08306937703583864 0.6204299212712205 chr11 135006516 10998393 0.08146564570261186 0.5969607261738784 chr12 133851895 11071771 0.08271658014255233 0.555101379014164 chr13 115169878 7793115 0.06766626079086409 0.501107347553974 chr14 107349540 7450069 0.06940010176103223 0.5424783999545314 chr15 102531392 7127413 0.06951444685350609 0.49129031893199276 chr16 90354753 7057781 0.07811189523145506 0.5639758416551246 chr17 81195210 6536966 0.0805092566421098 0.5407794449511999 chr18 78077248 6361980 0.0814831485863846 0.5991007309050802 chr19 59128983 4646233 0.07857792852618486 0.6063605611837787 chr20 63025520 5271024 0.08363316954782761 0.5650970473025061 chr21 48129895 3142653 0.0652952390608789 0.569561425377966 chr22 51304566 2808586 0.05474339262513204 0.45724558054617864 chrMT 16571 36824 2.222195401605214 3.6259776331304896 chrX 155270560 13942957 0.08979781485942989 0.6021646336896328 chrY 59373566 586064 0.009870789974110701 0.254563549571563