BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818853.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,509,284 number of mapped reads = 1,474,916 (97.72%) number of supplementary alignments = 23,332 (1.55%) number of secondary alignments = 0 number of mapped bases = 136,566,084 bp number of sequenced bases = 136,480,201 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 313,314 duplication rate = 18.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3213 >>>>>>> ACTG content number of A's = 39,692,536 bp (29.08%) number of C's = 28,654,152 bp (21%) number of T's = 39,652,209 bp (29.05%) number of G's = 28,479,324 bp (20.87%) number of N's = 1,980 bp (0%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 816,309 number of insertions = 19,424 mapped reads with insertion percentage = 1.28% number of deletions = 44,382 mapped reads with deletion percentage = 2.94% homopolymer indels = 40.79% >>>>>>> Coverage mean coverageData = 0.0441X std coverageData = 0.5053X There is a 3.12% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 12837194 0.05150315753877299 0.7530870498213083 chr2 243199373 10498452 0.043168088266411775 0.7301192735503451 chr3 198022430 8546024 0.04315684844388588 0.2742896711407596 chr4 191154276 6875688 0.03596931307987063 0.3093412835513751 chr5 180915260 6209346 0.03432184769819859 0.2572894533594825 chr6 171115067 6667074 0.03896251871262745 0.2836391256207185 chr7 159138663 12211798 0.07673683924314482 1.0423255696132208 chr8 146364022 11801495 0.08063111985266434 0.4667756400875229 chr9 141213431 4999911 0.035406766655219926 0.41901367613211926 chr10 135534747 6254463 0.046146564910030045 0.6524831821795805 chr11 135006516 5983025 0.04431656469084796 0.3366441832282972 chr12 133851895 5474610 0.040900504247623835 0.26757013423815346 chr13 115169878 4253728 0.03693437966479395 0.2530902826508531 chr14 107349540 3981389 0.037088086264738536 0.27668626831260196 chr15 102531392 3809239 0.037151929040425004 0.2520418083238349 chr16 90354753 3434157 0.03800748589285613 0.5267469131931374 chr17 81195210 3318285 0.04086798962648166 0.32608728324923825 chr18 78077248 2657051 0.03403105345106426 0.4568008976666284 chr19 59128983 2297924 0.038862904170024366 0.6072705702860438 chr20 63025520 5589246 0.08868226711973182 0.41572126096047446 chr21 48129895 1356154 0.02817695737753012 0.24553234896231207 chr22 51304566 1209317 0.023571332812755887 0.228386876309971 chrMT 16571 253213 15.280490012672741 10.004832547980406 chrX 155270560 5585543 0.03597296873277201 0.294548381002217 chrY 59373566 461758 0.007777164672911847 0.5547971426093699