BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081058.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,669,902 number of mapped reads = 2,431,911 (91.09%) number of supplementary alignments = 27,816 (1.04%) number of secondary alignments = 0 number of mapped bases = 163,981,881 bp number of sequenced bases = 163,921,281 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,744 duplication rate = 3.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8823 >>>>>>> ACTG content number of A's = 45,737,152 bp (27.9%) number of C's = 30,814,681 bp (18.8%) number of T's = 51,453,996 bp (31.39%) number of G's = 35,913,701 bp (21.91%) number of N's = 1,751 bp (0%) GC percentage = 40.71% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,487,454 number of insertions = 13,024 mapped reads with insertion percentage = 0.53% number of deletions = 36,848 mapped reads with deletion percentage = 1.5% homopolymer indels = 46.85% >>>>>>> Coverage mean coverageData = 0.053X std coverageData = 0.4128X There is a 4.41% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 14581245 0.05850033569224287 0.5964418540604314 chr2 243199373 11803140 0.04853277314987157 0.4576401723990776 chr3 198022430 13256277 0.06694331041185587 0.2992169309813592 chr4 191154276 9868876 0.05162780664137485 0.28467866095631555 chr5 180915260 9753748 0.05391335147737123 0.271492332565241 chr6 171115067 12116764 0.07081062008408646 0.45435424132830254 chr7 159138663 8377285 0.05264141876069425 0.4972499343460026 chr8 146364022 11923460 0.08146441889933853 0.5015574456219957 chr9 141213431 8357531 0.05918368345571888 0.5101640671945745 chr10 135534747 7243514 0.05344396297135524 0.4194052610437129 chr11 135006516 6492055 0.048086975298288565 0.3139396640500127 chr12 133851895 8535539 0.06376853312386799 0.3054548092510989 chr13 115169878 4380898 0.03803857463494057 0.22577026705918346 chr14 107349540 4925584 0.04588360602197271 0.3235694211979115 chr15 102531392 4551541 0.044391682500516526 0.243468806026592 chr16 90354753 4303437 0.04762823047062062 0.33303965218069365 chr17 81195210 3457608 0.04258389134038818 0.24533871320372286 chr18 78077248 4182378 0.053567180031755215 0.9311303163881093 chr19 59128983 3299899 0.05580848566260644 0.46103357203546197 chr20 63025520 2599698 0.04124833876816883 0.2515497559344676 chr21 48129895 3035543 0.06306980308184756 0.33664678817502147 chr22 51304566 1224570 0.02386863578575053 0.17621972468066852 chrMT 16571 170580 10.293886910868384 5.543833080316088 chrX 155270560 5109331 0.032905986814242186 0.24569978577819374 chrY 59373566 431380 0.007265522842269572 0.18357442362556517