BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818795.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 = 2,673,322 number of mapped reads = 2,603,705 (97.4%) number of supplementary alignments = 18,968 (0.71%) number of secondary alignments = 0 number of mapped bases = 177,031,246 bp number of sequenced bases = 176,958,466 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,301,210 duplication rate = 42.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5617 >>>>>>> ACTG content number of A's = 48,673,028 bp (27.51%) number of C's = 37,133,322 bp (20.98%) number of T's = 51,201,407 bp (28.93%) number of G's = 39,940,522 bp (22.57%) number of N's = 10,187 bp (0.01%) GC percentage = 43.55% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 878,916 number of insertions = 20,410 mapped reads with insertion percentage = 0.77% number of deletions = 44,674 mapped reads with deletion percentage = 1.7% homopolymer indels = 41.08% >>>>>>> Coverage mean coverageData = 0.0572X std coverageData = 0.6933X There is a 2.35% of reference with a coverageData >= 1X There is a 1.25% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 14479583 0.0580924650935975 1.1225566908566624 chr2 243199373 15633179 0.06428132937661808 1.0699317071131023 chr3 198022430 12067051 0.06093779881400304 0.4931191190052876 chr4 191154276 11770852 0.06157775931729615 0.5782372245302427 chr5 180915260 10997839 0.06079000190475917 0.5077395489886152 chr6 171115067 10505394 0.06139374038874087 0.55381505871883 chr7 159138663 9683324 0.06084834330925603 0.6272323902425163 chr8 146364022 9137750 0.06243166780426408 0.5928358714671996 chr9 141213431 7683910 0.05441345023335634 0.584221355253556 chr10 135534747 8681752 0.06405554436900229 0.7286236458216013 chr11 135006516 8302166 0.06149455778860333 0.5714513368925632 chr12 133851895 8046979 0.06011852876643995 0.5251097382984252 chr13 115169878 5657555 0.04912356510441038 0.44250150512700687 chr14 107349540 5429121 0.050574236275255584 0.5014390864778865 chr15 102531392 5089916 0.04964251338750965 0.44980378288187195 chr16 90354753 5272496 0.05835327777388755 0.7255123298504799 chr17 81195210 4727935 0.058229235443814975 0.5261655027550318 chr18 78077248 4810753 0.061615299248252195 0.8035744570476951 chr19 59128983 3592681 0.06076006752898151 0.8910967067881642 chr20 63025520 3838548 0.06090466211147484 0.5308319025669871 chr21 48129895 2390179 0.049661005909113244 0.4777768413524467 chr22 51304566 2173939 0.04237320709427695 0.4548216235861233 chrMT 16571 3638 0.2195401605213928 0.7289504995886018 chrX 155270560 5443699 0.03505944075940732 0.43439925156813897 chrY 59373566 1611007 0.027133404788252064 1.0273531221154137