BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094013.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 19,558 number of mapped reads = 2,219 (11.35%) number of supplementary alignments = 58 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,039 number of mapped paired reads (second in pair) = 1,180 number of mapped paired reads (both in pair) = 2,032 number of mapped paired reads (singletons) = 187 number of mapped bases = 273,411 bp number of sequenced bases = 269,833 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,354 duplication rate = 27.52% >>>>>>> Insert size mean insert size = 185,382.9174 std insert size = 3,076,377.676 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 17.2966 >>>>>>> ACTG content number of A's = 70,959 bp (26.3%) number of C's = 55,990 bp (20.75%) number of T's = 68,070 bp (25.23%) number of G's = 74,784 bp (27.71%) number of N's = 30 bp (0.01%) GC percentage = 48.46% >>>>>>> Mismatches and indels general error rate = 0.0306 number of mismatches = 7,833 number of insertions = 136 mapped reads with insertion percentage = 5.45% number of deletions = 501 mapped reads with deletion percentage = 21.27% homopolymer indels = 35.48% >>>>>>> Coverage mean coverageData = 0.0001X std coverageData = 0.0875X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 1950 7.823450919305834E-6 0.0037824363231153033 chr2 243199373 23340 9.597064216115393E-5 0.08109897159623847 chr3 198022430 7934 4.0066168261847915E-5 0.01598989061333983 chr4 191154276 4192 2.1929930565612878E-5 0.007872793724271894 chr5 180915260 1024 5.660108494993734E-6 0.002963627398048199 chr6 171115067 3274 1.913332389368144E-5 0.007636947179025757 chr7 159138663 2819 1.771411137216856E-5 0.00955792809013604 chr8 146364022 1479 1.0104942319773093E-5 0.003964969975687998 chr9 141213431 1136 8.044560577244242E-6 0.0035890314004901956 chr10 135534747 5201 3.8373923404306056E-5 0.021582865665659843 chr11 135006516 2186 1.6191811067845052E-5 0.007482621843415063 chr12 133851895 5933 4.432511022724034E-5 0.01607887196048175 chr13 115169878 1295 1.1244259545017491E-5 0.005691705599699815 chr14 107349540 1973 1.837921243071931E-5 0.008695545204809339 chr15 102531392 1598 1.5585470642981226E-5 0.005495033023839868 chr16 90354753 886 9.805792950371963E-6 0.004559018847932902 chr17 81195210 5923 7.294765294652234E-5 0.01761733278599668 chr18 78077248 1845 2.363044353202613E-5 0.008956993255821378 chr19 59128983 883 1.4933454884552977E-5 0.00483974650213786 chr20 63025520 790 1.2534605029835533E-5 0.006176011818894588 chr21 48129895 1597 3.318104059857185E-5 0.013520972211241591 chr22 51304566 1242 2.4208371629145056E-5 0.006224825665292567 chrMT 16571 102770 6.201798322370406 35.2685035027442 chrX 155270560 90886 5.853395518120113E-4 0.061305815894953576 chrY 59373566 1255 2.1137352605703354E-5 0.007092823701270049