BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506319.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 4,062,932 number of mapped reads = 2,870,940 (70.66%) number of supplementary alignments = 36,202 (0.89%) number of secondary alignments = 0 number of mapped bases = 227,883,828 bp number of sequenced bases = 227,787,723 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 346,153 duplication rate = 9.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8102 >>>>>>> ACTG content number of A's = 58,533,238 bp (25.7%) number of C's = 44,104,058 bp (19.36%) number of T's = 67,920,953 bp (29.82%) number of G's = 57,178,377 bp (25.1%) number of N's = 51,097 bp (0.02%) GC percentage = 44.46% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,671,951 number of insertions = 18,409 mapped reads with insertion percentage = 0.62% number of deletions = 46,392 mapped reads with deletion percentage = 1.59% homopolymer indels = 42.2% >>>>>>> Coverage mean coverageData = 0.0736X std coverageData = 0.5772X There is a 5.1% of reference with a coverageData >= 1X There is a 1.37% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 17022270 0.0682937917334216 0.9304704091247005 chr2 243199373 18461890 0.07591257235683745 0.6639187412262785 chr3 198022430 14026886 0.0708348342154977 0.36157796213817966 chr4 191154276 13997373 0.07322552910090277 0.5378898628004903 chr5 180915260 16897548 0.09340034665953552 0.4221870911809016 chr6 171115067 8305141 0.04853541622959479 0.3232458959102249 chr7 159138663 11628987 0.07307455511298346 0.717973581852583 chr8 146364022 14536166 0.09931515820192478 0.6526755584898112 chr9 141213431 6399310 0.04531658182003948 0.5903703530323554 chr10 135534747 13519210 0.09974718881498336 0.7299405511522341 chr11 135006516 9816881 0.07271412736848938 0.557255677583127 chr12 133851895 9659309 0.07216415576335322 0.3739784750184525 chr13 115169878 4533548 0.039364008009108074 0.2627735962374093 chr14 107349540 6529713 0.06082665095723745 0.3754229633345651 chr15 102531392 8504170 0.08294211006127762 0.4047759762590672 chr16 90354753 8608242 0.0952716012626364 0.5007347177087502 chr17 81195210 6027744 0.0742376797843124 0.4398622452895234 chr18 78077248 3900323 0.04995466797190393 0.7741135619691202 chr19 59128983 5763783 0.09747813521500953 0.7554793085066431 chr20 63025520 6468145 0.10262739601355134 0.47221503812344096 chr21 48129895 3844470 0.07987696628052066 0.4842802576481604 chr22 51304566 2886414 0.05626037261478832 0.34348515194808743 chrMT 16571 6770 0.40854504857884255 0.7789931050776167 chrX 155270560 15638024 0.10071467508071073 0.5032703675944594 chrY 59373566 901511 0.015183709868462339 0.5773594295315924