BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548985.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 = 7,802,047 number of mapped reads = 3,430,435 (43.97%) number of secondary alignments = 0 number of mapped bases = 135,660,922 bp number of sequenced bases = 135,643,981 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,683 duplication rate = 1.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8574 >>>>>>> ACTG content number of A's = 39,598,531 bp (29.19%) number of C's = 27,960,682 bp (20.61%) number of T's = 39,946,717 bp (29.45%) number of G's = 28,130,755 bp (20.74%) number of N's = 7,296 bp (0.01%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 400,195 number of insertions = 4,812 mapped reads with insertion percentage = 0.14% number of deletions = 13,257 mapped reads with deletion percentage = 0.39% homopolymer indels = 43.02% >>>>>>> Coverage mean coverageData = 0.0438X std coverageData = 0.3283X There is a 3.91% of reference with a coverageData >= 1X There is a 0.37% 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% 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 11000551 0.0441344978634978 0.5959436606313309 chr2 243199373 11727552 0.04822196642752035 0.3037210482304672 chr3 198022430 9442356 0.04768326497154893 0.23879957615160485 chr4 191154276 9070320 0.047450259496156916 0.24114570891250747 chr5 180915260 8514665 0.04706438251809162 0.2391675858829766 chr6 171115067 8184821 0.04783226365449163 0.27724818253941236 chr7 159138663 7736317 0.0486136860405821 0.5050207829813846 chr8 146364022 7120237 0.04864745381211238 0.40661253347249543 chr9 141213431 5753338 0.040742144421092634 0.27883478508320286 chr10 135534747 6406025 0.047264816895994946 0.27764423685298645 chr11 135006516 6270227 0.046443884234446876 0.28548056348493683 chr12 133851895 6233771 0.04657215349846186 0.24094526006850547 chr13 115169878 4498124 0.0390564275843029 0.21421728454284217 chr14 107349540 4269388 0.03977090167316972 0.24100404491601235 chr15 102531392 4028616 0.03929153717136699 0.21583057149521945 chr16 90354753 3797926 0.04203349435308622 0.2345599027558497 chr17 81195210 3545973 0.04367219445580595 0.24252210157463475 chr18 78077248 3679750 0.04712960682220767 0.42743605194948375 chr19 59128983 2635100 0.04456528535253177 0.47963212245448683 chr20 63025520 2784495 0.04418043675006569 0.2351970362537947 chr21 48129895 1768287 0.036739889002458864 0.2258620335088311 chr22 51304566 1543448 0.030084027998599577 0.21525853676031897 chrMT 16571 1753 0.1057872186349647 0.32807179530473796 chrX 155270560 4595694 0.029597974013876167 0.21850495722396113 chrY 59373566 1052188 0.017721489054573547 0.1854169243389841