BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231734.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 = 1,125,177 number of mapped reads = 997,827 (88.68%) number of supplementary alignments = 3,600 (0.32%) number of secondary alignments = 0 number of mapped bases = 65,950,167 bp number of sequenced bases = 65,936,924 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 396,153 duplication rate = 3.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5406 >>>>>>> ACTG content number of A's = 9,503,110 bp (14.41%) number of C's = 6,396,317 bp (9.7%) number of T's = 12,609,112 bp (19.12%) number of G's = 37,421,552 bp (56.75%) number of N's = 6,833 bp (0.01%) GC percentage = 66.45% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 433,825 number of insertions = 3,644 mapped reads with insertion percentage = 0.36% number of deletions = 8,552 mapped reads with deletion percentage = 0.85% homopolymer indels = 43.46% >>>>>>> Coverage mean coverageData = 0.0213X std coverageData = 55.4632X There is a 1.1% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 3769473 0.01512322410623001 0.17269345703450123 chr2 243199373 30343189 0.1247667238023677 197.8794259378672 chr3 198022430 3545114 0.017902588105801955 0.1483301697186352 chr4 191154276 2202168 0.011520370070089355 0.12490926052218845 chr5 180915260 2201060 0.012166248441397371 0.1216657181273741 chr6 171115067 3206938 0.018741412175001516 0.16717865525308703 chr7 159138663 2165002 0.013604500372106306 0.204089378123764 chr8 146364022 1606327 0.010974876052531543 0.13526920665143025 chr9 141213431 1333829 0.009445482561782667 0.12330912878323512 chr10 135534747 1237478 0.009130337624786359 0.1141390010006107 chr11 135006516 1604264 0.01188286349082588 0.2915073807879019 chr12 133851895 1029217 0.007689222479816218 0.09729417308605204 chr13 115169878 899178 0.007807406030246902 0.09756105508845218 chr14 107349540 1492079 0.013899258441163326 0.4368237701147036 chr15 102531392 820602 0.00800342201537652 0.10136202205835768 chr16 90354753 1001820 0.011087629225216299 0.12064930844415324 chr17 81195210 1052332 0.012960518237467456 0.1306475581342789 chr18 78077248 1126911 0.01443328279193447 0.2017606305428674 chr19 59128983 1041849 0.01761993775539823 0.16908614513702142 chr20 63025520 764704 0.01213324380346247 0.1259714714865994 chr21 48129895 947680 0.019690049188763034 0.15896813262943038 chr22 51304566 484560 0.00944477339502297 0.10696126757467246 chrMT 16571 959 0.05787218634964697 0.2516616162309687 chrX 155270560 1979717 0.012750111804839244 0.1324347982057029 chrY 59373566 93717 0.0015784297005168933 0.04670848027828022