BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063534.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 = 2,366,641 number of mapped reads = 2,096,338 (88.58%) number of supplementary alignments = 19,825 (0.84%) number of secondary alignments = 0 number of mapped bases = 136,877,152 bp number of sequenced bases = 136,810,503 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,454 duplication rate = 5.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9371 >>>>>>> ACTG content number of A's = 37,766,061 bp (27.6%) number of C's = 24,904,742 bp (18.2%) number of T's = 43,731,531 bp (31.97%) number of G's = 30,405,328 bp (22.22%) number of N's = 2,841 bp (0%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,095,049 number of insertions = 10,636 mapped reads with insertion percentage = 0.5% number of deletions = 40,252 mapped reads with deletion percentage = 1.9% homopolymer indels = 46.06% >>>>>>> Coverage mean coverageData = 0.0442X std coverageData = 0.4395X There is a 3.35% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% 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 14122383 0.05665936936622517 0.9001094647996758 chr2 243199373 13546094 0.055699543271437627 0.5914337761011245 chr3 198022430 9508508 0.048017328138029614 0.27439414454039956 chr4 191154276 4966827 0.025983342376290866 0.21776040215826864 chr5 180915260 5707648 0.031548737237533195 0.225411971034285 chr6 171115067 9943969 0.05811276104634316 0.3583141230580641 chr7 159138663 4963349 0.031188831842831305 0.2533614441990916 chr8 146364022 2023536 0.01382536481540525 0.6435468015036573 chr9 141213431 4861867 0.034429210915497124 0.3675652035431921 chr10 135534747 9533191 0.0703376160801038 0.43169257333835476 chr11 135006516 904800 0.006701898743909516 0.15059328422194895 chr12 133851895 8174993 0.06107491418033342 0.31448452975343427 chr13 115169878 4225048 0.0366853562178819 0.24546841609262143 chr14 107349540 5423326 0.050520253743052836 0.29613933438544787 chr15 102531392 3008730 0.029344476275129476 0.2193340279662585 chr16 90354753 2685458 0.02972126989268622 0.2327278235003268 chr17 81195210 5350296 0.0658942319380663 0.32934929193835544 chr18 78077248 4521839 0.057914938292907045 0.5561262702905213 chr19 59128983 3918756 0.06627470660200599 0.60250408771399 chr20 63025520 3167128 0.05025151716320627 0.28351539363340766 chr21 48129895 2267451 0.0471110730659188 0.2833077389447342 chr22 51304566 1496881 0.029176369994046925 0.2116855222616906 chrMT 16571 42773 2.581196065415485 2.384479310419772 chrX 155270560 12065949 0.07770918711183884 0.43014630990571456 chrY 59373566 446352 0.0075176889324788075 0.20806508835682203