BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046436.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 9,540,400 number of mapped reads = 9,483,508 (99.4%) number of supplementary alignments = 72,534 (0.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,744,765 number of mapped paired reads (second in pair) = 4,738,743 number of mapped paired reads (both in pair) = 9,447,170 number of mapped paired reads (singletons) = 36,338 number of mapped bases = 902,649,783 bp number of sequenced bases = 902,434,863 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,291,951 duplication rate = 31.45% >>>>>>> Insert size mean insert size = 15,780.5592 std insert size = 1,372,815.9773 median insert size = 123 >>>>>>> Mapping quality mean mapping quality = 50.5347 >>>>>>> ACTG content number of A's = 272,126,254 bp (30.15%) number of C's = 180,219,766 bp (19.97%) number of T's = 270,431,430 bp (29.97%) number of G's = 179,575,526 bp (19.9%) number of N's = 81,887 bp (0.01%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 3,160,183 number of insertions = 56,784 mapped reads with insertion percentage = 0.59% number of deletions = 72,410 mapped reads with deletion percentage = 0.75% homopolymer indels = 47.35% >>>>>>> Coverage mean coverageData = 0.2916X std coverageData = 76.8234X There is a 1.5% of reference with a coverageData >= 1X There is a 1.04% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% 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 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 127542628 0.5117043539883498 89.20273570794504 chr2 243199373 26701931 0.10979440724133775 12.649113135058935 chr3 198022430 7990388 0.04035092388271369 2.5926962115527856 chr4 191154276 32813764 0.17166115603921933 41.672617749194025 chr5 180915260 18489319 0.1021987807993643 5.2606321254666675 chr6 171115067 168060343 0.9821481295974948 130.06360715488745 chr7 159138663 123707791 0.7773584914434024 127.67304190150571 chr8 146364022 229108633 1.5653343620196498 242.62326766274222 chr9 141213431 6341890 0.044909963273960816 2.3331023148944605 chr10 135534747 27907443 0.20590618728937457 51.73975539796513 chr11 135006516 7674577 0.056845974752803785 1.8803972768790955 chr12 133851895 10792684 0.08063153681910891 9.053834694011282 chr13 115169878 2179969 0.018928291302001726 1.125033452325232 chr14 107349540 6663275 0.06207082955362454 5.548230505324813 chr15 102531392 3653158 0.03562965379422529 2.2028337413374315 chr16 90354753 7634062 0.08448987736151523 10.209660377964452 chr17 81195210 7439329 0.09162275705672786 8.543085606802757 chr18 78077248 3374492 0.04321991471830564 1.0893466068708857 chr19 59128983 1955424 0.03307048254153128 1.5243482849035992 chr20 63025520 2081209 0.033021687088024027 2.314513136951875 chr21 48129895 1200266 0.024938055651274535 1.9509287358308647 chr22 51304566 2033106 0.039628168767668746 4.120312266908216 chrMT 16571 330862 19.966326715346085 8.723172947574916 chrX 155270560 76818199 0.49473769528492717 95.25047519809154 chrY 59373566 155041 0.0026112799086381302 0.12793747924943683