BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089666.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 5,931,467 number of mapped reads = 2,607,955 (43.97%) number of supplementary alignments = 116 (0%) number of secondary alignments = 0 number of mapped bases = 120,016,007 bp number of sequenced bases = 119,992,672 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,561 duplication rate = 1.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.7318 >>>>>>> ACTG content number of A's = 35,589,431 bp (29.66%) number of C's = 25,434,956 bp (21.2%) number of T's = 34,037,125 bp (28.37%) number of G's = 24,862,938 bp (20.72%) number of N's = 68,222 bp (0.06%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.0133 number of mismatches = 1,580,700 number of insertions = 8,499 mapped reads with insertion percentage = 0.33% number of deletions = 16,140 mapped reads with deletion percentage = 0.62% homopolymer indels = 37.77% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.2866X There is a 3.35% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 10132718 0.04065272920623937 0.33230610088485246 chr2 243199373 11478256 0.04719689799529212 0.3975994854038934 chr3 198022430 11193785 0.05652786404045239 0.2763107941777415 chr4 191154276 4824398 0.025238242643340084 0.18091059308187835 chr5 180915260 5245688 0.028995276573131532 0.1923184261750731 chr6 171115067 7562856 0.044197487296662195 0.263430608361817 chr7 159138663 8088206 0.05082489602165377 0.45046874919245006 chr8 146364022 9376994 0.0640662498328995 0.4190701620395568 chr9 141213431 4287614 0.03036265013630325 0.25408647649496474 chr10 135534747 5003495 0.03691669561311831 0.26904150034859714 chr11 135006516 5820143 0.043110089590046155 0.27143630140654007 chr12 133851895 3963541 0.02961139250213828 0.19925137964841433 chr13 115169878 3527691 0.030630326794302935 0.19673411789328657 chr14 107349540 3985776 0.037128952764958284 0.23132680179290416 chr15 102531392 2990476 0.029166442995331616 0.19173209275899095 chr16 90354753 2355439 0.026068789098455065 0.1958380001163549 chr17 81195210 2739535 0.033740106097391705 0.22079182845119666 chr18 78077248 5768313 0.07387956348051612 0.4045941056827015 chr19 59128983 2047916 0.03463472388828335 0.318141836247185 chr20 63025520 2593432 0.041148918723716996 0.23413699029665017 chr21 48129895 1904215 0.039564079664000926 0.23345583291456623 chr22 51304566 932524 0.018176237959015188 0.14992090374498168 chrMT 16571 36707 2.2151348741777803 2.3304924713849173 chrX 155270560 3822375 0.024617512811185842 0.2179366013452777 chrY 59373566 333914 0.005623950564128151 0.1030619765948692