BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240069.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 = 1,878,397 number of mapped reads = 965,905 (51.42%) number of supplementary alignments = 8,016 (0.43%) number of secondary alignments = 0 number of mapped bases = 60,309,935 bp number of sequenced bases = 60,288,213 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 142,771 duplication rate = 11.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.817 >>>>>>> ACTG content number of A's = 16,056,562 bp (26.63%) number of C's = 10,802,725 bp (17.92%) number of T's = 19,327,654 bp (32.06%) number of G's = 14,060,355 bp (23.32%) number of N's = 40,917 bp (0.07%) GC percentage = 41.24% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 526,317 number of insertions = 4,183 mapped reads with insertion percentage = 0.43% number of deletions = 12,915 mapped reads with deletion percentage = 1.32% homopolymer indels = 47.35% >>>>>>> Coverage mean coverageData = 0.0195X std coverageData = 0.2722X There is a 1.17% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 5279593 0.021181864979184947 0.47457684419361507 chr2 243199373 5316051 0.02185881869029325 0.32780752012604836 chr3 198022430 3820878 0.019295177824047507 0.2116552139306844 chr4 191154276 4107646 0.02148864302674558 0.23013611299544096 chr5 180915260 3256826 0.018001941903629356 0.20269870769380904 chr6 171115067 3748065 0.02190376958447499 0.2376112031920884 chr7 159138663 3284811 0.020641187616361963 0.25333386275002506 chr8 146364022 3297556 0.022529826353091063 0.34095824248614676 chr9 141213431 2570615 0.01820375711995837 0.2530555634039327 chr10 135534747 2597178 0.01916245138230125 0.23400046636083516 chr11 135006516 2545723 0.01885629727679218 0.22917062211618955 chr12 133851895 2673788 0.019975720179381845 0.2165417218787578 chr13 115169878 1728449 0.01500782175005864 0.18781851169820704 chr14 107349540 2030226 0.01891229342948279 0.21718688202374714 chr15 102531392 1783251 0.01739224412363386 0.2084425578989195 chr16 90354753 1543101 0.01707824933127757 0.20031464756448586 chr17 81195210 1529832 0.018841407023887247 0.21300049091341414 chr18 78077248 1839143 0.02355542808066186 0.38001099248532927 chr19 59128983 1271472 0.021503363249119303 0.319364134871981 chr20 63025520 1233848 0.019576958666901914 0.21604333372856863 chr21 48129895 735353 0.01527850829510432 0.19058565076939377 chr22 51304566 603608 0.011765190645994355 0.16088971233810348 chrMT 16571 88048 5.313378794279163 4.543251699503922 chrX 155270560 3266079 0.021034760227566642 0.23532824317086076 chrY 59373566 158795 0.00267450669882284 0.075176248821077