BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237257.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,893,304 number of mapped reads = 2,668,818 (92.24%) number of supplementary alignments = 30,826 (1.07%) number of secondary alignments = 0 number of mapped bases = 168,497,248 bp number of sequenced bases = 168,429,792 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 482,057 duplication rate = 14.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4107 >>>>>>> ACTG content number of A's = 43,368,049 bp (25.75%) number of C's = 29,873,347 bp (17.74%) number of T's = 55,359,425 bp (32.87%) number of G's = 39,810,417 bp (23.64%) number of N's = 18,554 bp (0.01%) GC percentage = 41.37% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 998,214 number of insertions = 13,860 mapped reads with insertion percentage = 0.51% number of deletions = 38,113 mapped reads with deletion percentage = 1.41% homopolymer indels = 43.85% >>>>>>> Coverage mean coverageData = 0.0544X std coverageData = 0.7057X There is a 3.52% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 13221078 0.05304331017093033 0.9327544226008491 chr2 243199373 14045798 0.05775425251610332 1.4293549543094612 chr3 198022430 11030435 0.05570295748819969 0.3417463976165151 chr4 191154276 11051105 0.05781249172788581 0.5298499425787739 chr5 180915260 10103948 0.05584906436306147 0.34398157002996904 chr6 171115067 9988361 0.058372188814910145 0.547713435383971 chr7 159138663 9225929 0.05797415176222764 0.688040660334178 chr8 146364022 8739040 0.059707569391609094 1.0749596843132923 chr9 141213431 6956443 0.04926190767222418 0.46585433153129047 chr10 135534747 8041700 0.059333124368469145 0.6696056188762549 chr11 135006516 7677691 0.056869040306173076 0.46270622579281107 chr12 133851895 7373574 0.055087557781681014 0.35023399160037155 chr13 115169878 5172968 0.044915980548316636 0.3744963507310662 chr14 107349540 5162569 0.04809120747047449 0.33788805893789825 chr15 102531392 4733702 0.04616831886960045 0.3392485770003279 chr16 90354753 4666095 0.05164194295346035 0.3669089381837204 chr17 81195210 4495138 0.05536210818347535 0.37932646614529963 chr18 78077248 4606579 0.0590002736776788 1.2861538788332376 chr19 59128983 3371413 0.0570179432986358 0.6277902716587033 chr20 63025520 3468313 0.055030295664359456 0.3946347009109064 chr21 48129895 2257612 0.04690664710571257 0.38952824591495466 chr22 51304566 1895271 0.03694156578578211 0.2656631243349296 chrMT 16571 479169 28.91611852030656 21.716587687811792 chrX 155270560 10046655 0.06470418474693464 0.4228347989323925 chrY 59373566 686662 0.01156511299995018 0.4148490819930475