BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549085.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 = 7,981,392 number of mapped reads = 6,973,326 (87.37%) number of secondary alignments = 0 number of mapped bases = 276,931,738 bp number of sequenced bases = 276,905,570 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 217,820 duplication rate = 2.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7868 >>>>>>> ACTG content number of A's = 83,025,429 bp (29.98%) number of C's = 55,806,418 bp (20.15%) number of T's = 83,916,815 bp (30.31%) number of G's = 54,090,219 bp (19.53%) number of N's = 66,689 bp (0.02%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,089,731 number of insertions = 6,455 mapped reads with insertion percentage = 0.09% number of deletions = 20,874 mapped reads with deletion percentage = 0.3% homopolymer indels = 45.75% >>>>>>> Coverage mean coverageData = 0.0895X std coverageData = 0.6577X There is a 7.69% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.13% 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 0.01% 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 22463006 0.09012216663644741 1.5133989814047768 chr2 243199373 24352755 0.10013494154855407 0.5131580475951893 chr3 198022430 19833015 0.10015539653765484 0.36090868255564196 chr4 191154276 19784482 0.10350007550968936 0.3667207282187909 chr5 180915260 18234392 0.10078968462914627 0.36985703391979075 chr6 171115067 17143742 0.10018838376167073 0.4828713873688092 chr7 159138663 15503743 0.09742285568906658 0.6974872787342161 chr8 146364022 14839616 0.10138841360891271 0.9512660620591721 chr9 141213431 11776632 0.08339597669006428 0.4906257474865752 chr10 135534747 13025264 0.09610276544065854 0.5345891142374242 chr11 135006516 12858385 0.09524269924867923 0.5281951459624512 chr12 133851895 12754318 0.09528679440810307 0.3607381696797812 chr13 115169878 9624678 0.08356940345113503 0.317543734216995 chr14 107349540 8688056 0.08093240082817309 0.3647989948469968 chr15 102531392 7891834 0.07696992936563272 0.30664104140385645 chr16 90354753 7111439 0.07870575441670456 0.3817440370070024 chr17 81195210 6370014 0.07845307623442319 0.3569695188788967 chr18 78077248 7812993 0.10006747420195958 0.9351780248299265 chr19 59128983 4195115 0.07094853973727233 1.1629895993401085 chr20 63025520 5362778 0.0850889925223941 0.33619821235429165 chr21 48129895 3677085 0.07639919014990579 0.3585652268586052 chr22 51304566 2526862 0.049252185468248576 0.28064640382158385 chrMT 16571 10836 0.6539134632792227 1.0965355818053493 chrX 155270560 8931188 0.05752016351328932 0.3495067617679147 chrY 59373566 2159510 0.036371573167762905 0.32343154477214087