BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230383.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 = 2,786,951 number of mapped reads = 2,528,143 (90.71%) number of supplementary alignments = 25,014 (0.9%) number of secondary alignments = 0 number of mapped bases = 175,718,238 bp number of sequenced bases = 175,641,766 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 198,869 duplication rate = 5.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7181 >>>>>>> ACTG content number of A's = 51,212,328 bp (29.16%) number of C's = 34,641,768 bp (19.72%) number of T's = 52,746,801 bp (30.03%) number of G's = 36,904,024 bp (21.01%) number of N's = 136,845 bp (0.08%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,672,165 number of insertions = 16,900 mapped reads with insertion percentage = 0.66% number of deletions = 45,027 mapped reads with deletion percentage = 1.76% homopolymer indels = 47.39% >>>>>>> Coverage mean coverageData = 0.0568X std coverageData = 0.7332X There is a 2.64% of reference with a coverageData >= 1X There is a 1.28% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 16323648 0.0654909020266794 1.4214346571709238 chr2 243199373 10690721 0.04395867007436734 0.747018592217183 chr3 198022430 15843571 0.08000897171093194 0.5187307551099801 chr4 191154276 8207809 0.042938139662646105 0.5099795720583381 chr5 180915260 10741512 0.05937316730495813 0.44632061847061427 chr6 171115067 8960935 0.05236788996494388 0.4538698915654591 chr7 159138663 8236888 0.051759188149016935 0.6877228351721033 chr8 146364022 10979962 0.07501817625645735 1.040208685789124 chr9 141213431 8364996 0.05923654669930086 0.7123958850317691 chr10 135534747 8990142 0.06633090184615167 0.7291055119060557 chr11 135006516 7853877 0.05817405879876198 0.6222449387218131 chr12 133851895 5694759 0.04254522507880819 0.3881483229707513 chr13 115169878 6757217 0.05867173880309225 0.44828361225373364 chr14 107349540 5975853 0.05566724366028956 0.47689305896925327 chr15 102531392 4830405 0.04711147391815377 0.3899006118924054 chr16 90354753 4116022 0.04555401750697055 0.4801401002343645 chr17 81195210 5171142 0.06368777172939143 0.5214629558340489 chr18 78077248 7669949 0.09823539118591884 1.439485815972153 chr19 59128983 3212138 0.054324255839137296 0.9466091195236543 chr20 63025520 1792041 0.02843357738262215 0.3498779713385018 chr21 48129895 2208035 0.0458765804496353 0.4829716374655791 chr22 51304566 1412662 0.027534820195145984 0.285855098004213 chrMT 16571 15484 0.9344034759519643 1.8310180662036175 chrX 155270560 11019682 0.07097083954614448 0.5503477320571267 chrY 59373566 648788 0.010927219699082922 0.3910310490296892