BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927033.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 34,415,054 number of mapped reads = 33,955,297 (98.66%) number of supplementary alignments = 151,181 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,055,392 number of mapped paired reads (second in pair) = 16,899,905 number of mapped paired reads (both in pair) = 33,696,040 number of mapped paired reads (singletons) = 259,257 number of mapped bases = 3,253,107,034 bp number of sequenced bases = 3,250,716,627 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,226,239 duplication rate = 5.24% >>>>>>> Insert size mean insert size = 47,199.5177 std insert size = 2,107,376.1399 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 53.9059 >>>>>>> ACTG content number of A's = 940,013,092 bp (28.92%) number of C's = 651,709,316 bp (20.05%) number of T's = 947,096,513 bp (29.14%) number of G's = 711,347,336 bp (21.88%) number of N's = 550,370 bp (0.02%) GC percentage = 41.93% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 34,444,721 number of insertions = 505,407 mapped reads with insertion percentage = 1.46% number of deletions = 1,724,499 mapped reads with deletion percentage = 4.95% homopolymer indels = 53.41% >>>>>>> Coverage mean coverageData = 1.0508X std coverageData = 3.8184X There is a 35.52% of reference with a coverageData >= 1X There is a 21.65% of reference with a coverageData >= 2X There is a 13.78% of reference with a coverageData >= 3X There is a 9.22% of reference with a coverageData >= 4X There is a 6.34% of reference with a coverageData >= 5X There is a 4.47% of reference with a coverageData >= 6X There is a 3.2% of reference with a coverageData >= 7X There is a 2.33% of reference with a coverageData >= 8X There is a 1.71% of reference with a coverageData >= 9X There is a 1.27% of reference with a coverageData >= 10X There is a 0.96% of reference with a coverageData >= 11X There is a 0.72% of reference with a coverageData >= 12X There is a 0.55% of reference with a coverageData >= 13X There is a 0.42% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.2% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% 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 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 252605312 1.0134591078912498 5.8636589906966 chr2 243199373 298453281 1.2271959311342469 6.656386292498475 chr3 198022430 240334184 1.2136715219583962 2.347925923160744 chr4 191154276 186121635 0.9736723598063797 2.8316393653213052 chr5 180915260 198523358 1.0973278760453928 2.205537780577796 chr6 171115067 183386733 1.0717158705843244 2.2013012688076983 chr7 159138663 170412470 1.0708426650536833 2.795370064696784 chr8 146364022 165044541 1.1276305388765553 2.546816148614362 chr9 141213431 131266835 0.9295633855111133 4.5743440190309075 chr10 135534747 153084859 1.1294879164824059 5.210714167470706 chr11 135006516 163862353 1.213736624386337 4.2124115219557625 chr12 133851895 147834624 1.1044641840894371 2.2538075170680476 chr13 115169878 97099305 0.8430963606647217 1.9246572720522468 chr14 107349540 96507501 0.8990024642862932 2.0647757776438986 chr15 102531392 97954130 0.9553574577432832 2.164652730226171 chr16 90354753 99673122 1.1031309221773866 4.964404068406726 chr17 81195210 81898428 1.008660831100751 3.395344518701944 chr18 78077248 88211511 1.1297979022006512 4.755082483604739 chr19 59128983 48258387 0.8161545244233273 3.3695636569445884 chr20 63025520 75200858 1.1931810796642377 2.571167767763636 chr21 48129895 40060823 0.8323480240295559 2.621418579344098 chr22 51304566 40714639 0.7935870464238992 2.0797038702645976 chrMT 16571 9621 0.5805926015327982 1.3632840900371237 chrX 155270560 192159927 1.2375812066369827 2.8581772909327188 chrY 59373566 4428597 0.07458869827694029 2.0465831795127563