BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083633.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,538,261 number of mapped reads = 2,113,379 (83.26%) number of supplementary alignments = 15,396 (0.61%) number of secondary alignments = 0 number of mapped bases = 127,235,304 bp number of sequenced bases = 127,193,744 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,883 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6141 >>>>>>> ACTG content number of A's = 37,826,584 bp (29.74%) number of C's = 24,783,871 bp (19.49%) number of T's = 37,533,717 bp (29.51%) number of G's = 27,032,445 bp (21.25%) number of N's = 17,127 bp (0.01%) GC percentage = 40.74% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,057,158 number of insertions = 9,150 mapped reads with insertion percentage = 0.43% number of deletions = 26,129 mapped reads with deletion percentage = 1.23% homopolymer indels = 45.74% >>>>>>> Coverage mean coverageData = 0.0411X std coverageData = 0.3463X There is a 3.62% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 9375742 0.03761572172773042 0.6872983522222725 chr2 243199373 11230339 0.04617749980794564 0.3130180834163369 chr3 198022430 9952875 0.05026135170647083 0.24672955963830628 chr4 191154276 7784896 0.040725722504894424 0.23406720230994174 chr5 180915260 8481099 0.04687884814138951 0.23895852159909287 chr6 171115067 7447044 0.043520679567042454 0.2643810259829291 chr7 159138663 7374736 0.046341573197708714 0.47542099583069725 chr8 146364022 6454784 0.04410089249938759 0.498919190654804 chr9 141213431 5132071 0.036342654970262706 0.2671503253562297 chr10 135534747 5400717 0.039847471733576924 0.3296121161695148 chr11 135006516 5805323 0.04300031711062005 0.2512598298401084 chr12 133851895 5853468 0.043730931116066754 0.23311032125592912 chr13 115169878 4320353 0.03751287294061387 0.21249184520412023 chr14 107349540 4155029 0.038705606004459825 0.22443282444971988 chr15 102531392 3768798 0.036757503497075315 0.21110490432576004 chr16 90354753 3371058 0.03730913856850453 0.23117791938987747 chr17 81195210 2792085 0.03438731176383435 0.20996195498237477 chr18 78077248 3229250 0.04135968009528205 0.4451327962714501 chr19 59128983 2103368 0.0355725380901613 0.4854163036713352 chr20 63025520 2280142 0.036178075167011714 0.21378869257403765 chr21 48129895 1551192 0.0322292828604758 0.20940099416161229 chr22 51304566 1294204 0.025225902895270567 0.1737121061510196 chrMT 16571 23186 1.3991913583972 1.5041138585530225 chrX 155270560 7690511 0.049529743436231566 0.2634568973173895 chrY 59373566 363034 0.006114404514628614 0.15265202243876322