BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238330.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 = 2,493,975 number of mapped reads = 2,244,765 (90.01%) number of supplementary alignments = 29,121 (1.17%) number of secondary alignments = 0 number of mapped bases = 149,703,806 bp number of sequenced bases = 149,638,888 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 150,911 duplication rate = 5.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8521 >>>>>>> ACTG content number of A's = 41,999,820 bp (28.07%) number of C's = 28,898,267 bp (19.31%) number of T's = 45,887,325 bp (30.67%) number of G's = 32,808,703 bp (21.93%) number of N's = 44,773 bp (0.03%) GC percentage = 41.24% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,253,889 number of insertions = 12,004 mapped reads with insertion percentage = 0.53% number of deletions = 37,478 mapped reads with deletion percentage = 1.65% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 0.0484X std coverageData = 0.4797X There is a 3.59% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 16108701 0.06462852904988349 0.7980125493905902 chr2 243199373 11588789 0.04765139341045916 0.603286288310652 chr3 198022430 8466204 0.04275376279343709 0.26312873051938174 chr4 191154276 9076607 0.04748314916062877 0.3505886947763087 chr5 180915260 12073393 0.06673507254169715 0.3330425414128169 chr6 171115067 8605722 0.05029201782681124 0.3432040585225099 chr7 159138663 6560670 0.041226122403705254 0.5459584594715938 chr8 146364022 5132558 0.03506707406551044 0.7785247158181728 chr9 141213431 5976969 0.042325782736629354 0.47134477855057844 chr10 135534747 6736795 0.049705298081236686 0.4220612978488928 chr11 135006516 5452240 0.04038501371296775 0.42619950003503315 chr12 133851895 6966320 0.05204498598992566 0.30166913182214616 chr13 115169878 2839641 0.024656108431407732 0.20029312791092813 chr14 107349540 4745030 0.0442016798581531 0.30721686099546414 chr15 102531392 4567433 0.044546678933218814 0.273262745493128 chr16 90354753 4105295 0.04543529658035809 0.30160013647647144 chr17 81195210 3586938 0.04417671929169221 0.30900302918027217 chr18 78077248 5429395 0.06953875987022494 0.8924009536845898 chr19 59128983 2928412 0.04952583067427356 0.5608091610277219 chr20 63025520 3911689 0.06206516027158523 0.33205199404779295 chr21 48129895 2067647 0.04295972388886367 0.3027305366613525 chr22 51304566 2070819 0.0403632495400117 0.25446087557450525 chrMT 16571 20214 1.219841892462736 1.6640032648949417 chrX 155270560 10216865 0.06580040028193368 0.37706182095181007 chrY 59373566 469460 0.007906885700616331 0.22366829609800698