BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549053.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 3,822,430 number of mapped reads = 3,304,657 (86.45%) number of secondary alignments = 0 number of mapped bases = 130,657,678 bp number of sequenced bases = 130,645,003 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,444 duplication rate = 2.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.4799 >>>>>>> ACTG content number of A's = 36,914,522 bp (28.26%) number of C's = 27,831,557 bp (21.3%) number of T's = 37,755,760 bp (28.9%) number of G's = 28,142,108 bp (21.54%) number of N's = 1,056 bp (0%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 363,852 number of insertions = 4,314 mapped reads with insertion percentage = 0.13% number of deletions = 9,736 mapped reads with deletion percentage = 0.29% homopolymer indels = 41.17% >>>>>>> Coverage mean coverageData = 0.0422X std coverageData = 0.3663X There is a 3.75% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 10648096 0.04272043920002912 0.5953731209759157 chr2 243199373 11241051 0.04622154597413374 0.3546793503070669 chr3 198022430 8833322 0.04460768408912061 0.23073255372576135 chr4 191154276 8745209 0.04574948142933512 0.25107321889728124 chr5 180915260 8252936 0.04561768863499961 0.23505863798369267 chr6 171115067 7532812 0.04402190953763294 0.23978870386389334 chr7 159138663 7399139 0.04649491745447176 0.5223046597291556 chr8 146364022 6686178 0.04568184112896269 0.6529536040310822 chr9 141213431 5525867 0.039131313224731436 0.3619342421937128 chr10 135534747 6269993 0.04626114807297349 0.3227489662766489 chr11 135006516 6024997 0.0446274533889905 0.28883956594200616 chr12 133851895 6059448 0.04526979614296832 0.24075319263051378 chr13 115169878 4277531 0.03714105696977468 0.2089976911291294 chr14 107349540 4057367 0.03779584896218465 0.2595895171800684 chr15 102531392 3730441 0.03638340343609107 0.2087731757168916 chr16 90354753 3776273 0.0417938500700677 0.25141418712761165 chr17 81195210 3511614 0.04324902909913036 0.23900855277361768 chr18 78077248 3466286 0.044395596525123426 0.5966679399479055 chr19 59128983 2798514 0.047328972324790365 0.5909318136857928 chr20 63025520 2756817 0.04374128130953937 0.23882765541161502 chr21 48129895 1722950 0.03579791728197205 0.252674513026173 chr22 51304566 1519681 0.029620774883857316 0.2441053921740328 chrMT 16571 7582 0.4575463158529962 0.8066647968359117 chrX 155270560 4635401 0.029853701822161266 0.2323497884560542 chrY 59373566 1178173 0.019843392933481543 0.21384735354491413