BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240270.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 = 2,451,038 number of mapped reads = 1,965,359 (80.18%) number of supplementary alignments = 11,045 (0.45%) number of secondary alignments = 0 number of mapped bases = 128,102,878 bp number of sequenced bases = 128,048,200 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,313 duplication rate = 3.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2015 >>>>>>> ACTG content number of A's = 35,807,455 bp (27.96%) number of C's = 23,299,272 bp (18.2%) number of T's = 39,503,832 bp (30.85%) number of G's = 29,405,321 bp (22.96%) number of N's = 32,320 bp (0.03%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,135,759 number of insertions = 9,415 mapped reads with insertion percentage = 0.47% number of deletions = 31,731 mapped reads with deletion percentage = 1.6% homopolymer indels = 46.92% >>>>>>> Coverage mean coverageData = 0.0414X std coverageData = 0.5291X There is a 3.5% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.08% 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 10828290 0.043443382233338546 1.314899764980675 chr2 243199373 10976050 0.04513190089515568 0.5401533796048158 chr3 198022430 9417145 0.04755595111119483 0.25112924163555417 chr4 191154276 9014519 0.047158343452385024 0.2644830591318549 chr5 180915260 6817079 0.03768106128803065 0.22757434532954218 chr6 171115067 7766067 0.04538505659469484 0.3242142274087893 chr7 159138663 7158708 0.044984090384119914 0.5762956069964891 chr8 146364022 7072073 0.048318383871686715 0.604011556570875 chr9 141213431 4789411 0.033916115245440075 0.4218122771930408 chr10 135534747 6615276 0.04880870881029497 0.3713939294849815 chr11 135006516 6164982 0.04566432926837398 0.3784793274580828 chr12 133851895 5241794 0.03916114896991186 0.23920297244575692 chr13 115169878 3841637 0.0333562652553995 0.21060176701177435 chr14 107349540 3457808 0.03221073886297044 0.23315744840791602 chr15 102531392 4068251 0.039678101707621406 0.2508913130286113 chr16 90354753 3526406 0.03902845044576681 0.2638057863380117 chr17 81195210 3113378 0.03834435553525879 0.26501377859732145 chr18 78077248 3411399 0.04369261324374547 0.7710741728610363 chr19 59128983 2957202 0.05001273233466572 0.7913283250526044 chr20 63025520 2432380 0.038593572889204245 0.24306708680954442 chr21 48129895 1768336 0.036740907080723945 0.238435140377583 chr22 51304566 1371613 0.026734715970504457 0.1866215003963408 chrMT 16571 13073 0.7889083338362199 1.144119660412446 chrX 155270560 5966802 0.03842841811094132 0.2821705181117421 chrY 59373566 313199 0.005275057927293773 0.11587884115692476