BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008672.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 = 2,071,087 number of mapped reads = 1,528,511 (73.8%) number of supplementary alignments = 4,997 (0.24%) number of secondary alignments = 0 number of mapped bases = 91,888,806 bp number of sequenced bases = 91,833,339 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 123,865 duplication rate = 6.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6691 >>>>>>> ACTG content number of A's = 23,978,438 bp (26.11%) number of C's = 15,666,149 bp (17.06%) number of T's = 29,450,088 bp (32.07%) number of G's = 22,724,161 bp (24.75%) number of N's = 14,503 bp (0.02%) GC percentage = 41.8% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 906,978 number of insertions = 7,269 mapped reads with insertion percentage = 0.47% number of deletions = 35,895 mapped reads with deletion percentage = 2.32% homopolymer indels = 48.74% >>>>>>> Coverage mean coverageData = 0.0297X std coverageData = 0.2901X There is a 2.34% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.04% 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 7950776 0.03189872092635629 0.40787078059560405 chr2 243199373 8042581 0.033069908449147194 0.3480737427697897 chr3 198022430 6607454 0.03336719986720696 0.2383739322874401 chr4 191154276 5387012 0.028181488338769885 0.21993616253864098 chr5 180915260 5368686 0.02967514183159563 0.21805856806038365 chr6 171115067 5360434 0.031326487456537065 0.26827290990247515 chr7 159138663 5266857 0.033096023937313084 0.4285383886395382 chr8 146364022 4985561 0.03406274938249511 0.303559282543803 chr9 141213431 3783899 0.02679560274971295 0.2852158551041521 chr10 135534747 4499354 0.03319705167561201 0.29809802276074865 chr11 135006516 4157038 0.03079138787641924 0.2912516324556298 chr12 133851895 4591084 0.0342997310572256 0.24282480334855502 chr13 115169878 2900402 0.025183685616129593 0.2077174697694761 chr14 107349540 2600425 0.02422390445268792 0.21151214474477853 chr15 102531392 2344078 0.02286205184847193 0.20509275900681564 chr16 90354753 2311540 0.025582937512982854 0.22879527430624771 chr17 81195210 2228629 0.02744778909987424 0.22898796299395646 chr18 78077248 2254179 0.028871137978633672 0.44119661050708 chr19 59128983 1553658 0.02627574365687974 0.2865314059786293 chr20 63025520 1845076 0.029275061911428896 0.22986616769262794 chr21 48129895 1177879 0.024472918546778463 0.21262614317529002 chr22 51304566 906942 0.017677607876070915 0.16800090539043816 chrMT 16571 67671 4.083700440528634 3.8048764048214068 chrX 155270560 5415888 0.03488032760363587 0.2702132520865649 chrY 59373566 281703 0.004744586168194782 0.10442391558751046