BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006411.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 9,015,608 number of mapped reads = 5,326,227 (59.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,687,814 number of mapped paired reads (second in pair) = 2,638,413 number of mapped paired reads (both in pair) = 4,770,642 number of mapped paired reads (singletons) = 555,585 number of mapped bases = 206,051,066 bp number of sequenced bases = 206,024,958 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 209,384 duplication rate = 3.31% >>>>>>> Insert size mean insert size = 85,764.887 std insert size = 2,797,771.6517 median insert size = 152 >>>>>>> Mapping quality mean mapping quality = 47.8349 >>>>>>> ACTG content number of A's = 57,544,513 bp (27.93%) number of C's = 44,186,553 bp (21.45%) number of T's = 58,631,821 bp (28.46%) number of G's = 45,653,186 bp (22.16%) number of N's = 8,885 bp (0%) GC percentage = 43.61% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 706,493 number of insertions = 5,946 mapped reads with insertion percentage = 0.11% number of deletions = 19,512 mapped reads with deletion percentage = 0.37% homopolymer indels = 43.09% >>>>>>> Coverage mean coverageData = 0.0666X std coverageData = 0.4411X There is a 5.65% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 17130450 0.06872781271826801 0.5272216161007295 chr2 243199373 17654266 0.07259174142689916 0.5865495125240804 chr3 198022430 13968921 0.07054211485032276 0.3000198045217347 chr4 191154276 13131810 0.06869744310611184 0.3297113435537367 chr5 180915260 11999596 0.06632716333602814 0.6516617152474649 chr6 171115067 11719808 0.06849080098831975 0.37507081388919344 chr7 159138663 11122267 0.06989041374565275 0.4262268873576419 chr8 146364022 10278740 0.07022723111558113 0.848231798283427 chr9 141213431 8573871 0.06071569070508598 0.31592487922351054 chr10 135534747 9828635 0.07251745561601262 0.39820967630267523 chr11 135006516 9482663 0.0702385579670836 0.3558520445450394 chr12 133851895 9235382 0.06899702092376055 0.2999025607534122 chr13 115169878 6341331 0.055060673069394064 0.26473406677853323 chr14 107349540 6351481 0.05916635506775343 0.3406534461779412 chr15 102531392 5915289 0.0576924674932727 0.27232589941785296 chr16 90354753 6314585 0.06988658360894417 0.34873885565097057 chr17 81195210 5683834 0.07000208509836972 0.3209627724128034 chr18 78077248 5314316 0.06806484777742167 0.49270505071567183 chr19 59128983 4384649 0.07415397284949075 0.4129577031890733 chr20 63025520 4540611 0.07204400693560323 0.3155805067465563 chr21 48129895 2702739 0.05615509861386567 0.32203058210507635 chr22 51304566 2640154 0.051460409975985374 0.2615810377863968 chrMT 16571 9808 0.5918773761390381 0.9011510985654612 chrX 155270560 11217547 0.0722451635390508 0.3310783448252052 chrY 59373566 508313 0.008561267820767242 0.19715604387369318