BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432717.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 367,188,438 number of mapped reads = 367,054,179 (99.96%) number of supplementary alignments = 2,672,236 (0.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 183,529,510 number of mapped paired reads (second in pair) = 183,524,669 number of mapped paired reads (both in pair) = 367,004,126 number of mapped paired reads (singletons) = 50,053 number of mapped bases = 51,753,838,340 bp number of sequenced bases = 51,699,805,700 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 184,083,392 duplication rate = 34.26% >>>>>>> Insert size mean insert size = 38,838.7508 std insert size = 1,979,655.1182 median insert size = 322 >>>>>>> Mapping quality mean mapping quality = 57.3057 >>>>>>> ACTG content number of A's = 14,482,589,413 bp (28.01%) number of C's = 10,967,899,908 bp (21.21%) number of T's = 14,322,097,980 bp (27.7%) number of G's = 11,919,341,476 bp (23.05%) number of N's = 7,876,923 bp (0.02%) GC percentage = 44.27% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 380,348,971 number of insertions = 11,263,895 mapped reads with insertion percentage = 3.01% number of deletions = 38,416,986 mapped reads with deletion percentage = 9.94% homopolymer indels = 53.58% >>>>>>> Coverage mean coverageData = 16.718X std coverageData = 54.5817X There is a 38.67% of reference with a coverageData >= 1X There is a 35.02% of reference with a coverageData >= 2X There is a 32.6% of reference with a coverageData >= 3X There is a 30.69% of reference with a coverageData >= 4X There is a 29.07% of reference with a coverageData >= 5X There is a 27.65% of reference with a coverageData >= 6X There is a 26.39% of reference with a coverageData >= 7X There is a 25.25% of reference with a coverageData >= 8X There is a 24.22% of reference with a coverageData >= 9X There is a 23.27% of reference with a coverageData >= 10X There is a 22.41% of reference with a coverageData >= 11X There is a 21.61% of reference with a coverageData >= 12X There is a 20.88% of reference with a coverageData >= 13X There is a 20.19% of reference with a coverageData >= 14X There is a 19.56% of reference with a coverageData >= 15X There is a 18.96% of reference with a coverageData >= 16X There is a 18.4% of reference with a coverageData >= 17X There is a 17.88% of reference with a coverageData >= 18X There is a 17.38% of reference with a coverageData >= 19X There is a 16.91% of reference with a coverageData >= 20X There is a 16.47% of reference with a coverageData >= 21X There is a 16.04% of reference with a coverageData >= 22X There is a 15.64% of reference with a coverageData >= 23X There is a 15.26% of reference with a coverageData >= 24X There is a 14.89% of reference with a coverageData >= 25X There is a 14.54% of reference with a coverageData >= 26X There is a 14.2% of reference with a coverageData >= 27X There is a 13.88% of reference with a coverageData >= 28X There is a 13.57% of reference with a coverageData >= 29X There is a 13.27% of reference with a coverageData >= 30X There is a 12.99% of reference with a coverageData >= 31X There is a 12.71% of reference with a coverageData >= 32X There is a 12.45% of reference with a coverageData >= 33X There is a 12.19% of reference with a coverageData >= 34X There is a 11.95% of reference with a coverageData >= 35X There is a 11.71% of reference with a coverageData >= 36X There is a 11.48% of reference with a coverageData >= 37X There is a 11.25% of reference with a coverageData >= 38X There is a 11.04% of reference with a coverageData >= 39X There is a 10.83% of reference with a coverageData >= 40X There is a 10.63% of reference with a coverageData >= 41X There is a 10.43% of reference with a coverageData >= 42X There is a 10.24% of reference with a coverageData >= 43X There is a 10.06% of reference with a coverageData >= 44X There is a 9.88% of reference with a coverageData >= 45X There is a 9.71% of reference with a coverageData >= 46X There is a 9.54% of reference with a coverageData >= 47X There is a 9.38% of reference with a coverageData >= 48X There is a 9.22% of reference with a coverageData >= 49X There is a 9.06% of reference with a coverageData >= 50X There is a 8.91% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4042223719 16.217507113051486 52.67337428075122 chr2 243199373 4666805829 19.18921817697285 60.72298532755983 chr3 198022430 4333567138 21.884223610426353 63.12902640894116 chr4 191154276 2145421471 11.22350760806418 39.085614169014654 chr5 180915260 2694323555 14.89273793155978 47.046253842376515 chr6 171115067 2387286114 13.951349555910234 45.83552988231529 chr7 159138663 3313466897 20.82125634673706 61.61994582581333 chr8 146364022 2582045882 17.641260787435865 52.81775460901785 chr9 141213431 1898439622 13.443761039982096 46.32132314701973 chr10 135534747 2515064367 18.55660207193953 54.583380313655454 chr11 135006516 2790430454 20.668857597954755 62.53813411985114 chr12 133851895 2352114758 17.572517430552626 53.763537489230956 chr13 115169878 1286057377 11.166612306387961 41.003566011745505 chr14 107349540 1768318288 16.472527856197615 55.542769244811446 chr15 102531392 1655704478 16.148268795570434 52.924509782491086 chr16 90354753 2588967321 28.65336061513001 85.0234515306646 chr17 81195210 1374466350 16.927924073353587 53.048137920872634 chr18 78077248 1698555610 21.75480890412531 62.83156839588924 chr19 59128983 1304991976 22.07025911472213 66.9858357546432 chr20 63025520 1874575753 29.74312235741966 78.3650816049131 chr21 48129895 604007346 12.549525528779983 47.2094824967099 chr22 51304566 838120937 16.336186081371395 56.14728343715232 chrMT 16571 5660034 341.5626093778287 526.4379657641744 chrX 155270560 992744334 6.393641743805136 29.03716499720899 chrY 59373566 40478730 0.6817634972438745 15.117862804970105