BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716175.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,252,616 number of mapped reads = 1,964,682 (87.22%) number of supplementary alignments = 55,786 (2.48%) number of secondary alignments = 0 number of mapped bases = 146,368,362 bp number of sequenced bases = 146,313,718 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,188 duplication rate = 2.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0156 >>>>>>> ACTG content number of A's = 37,320,145 bp (25.51%) number of C's = 28,902,357 bp (19.75%) number of T's = 45,002,263 bp (30.76%) number of G's = 35,071,568 bp (23.97%) number of N's = 17,385 bp (0.01%) GC percentage = 43.72% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,073,079 number of insertions = 12,382 mapped reads with insertion percentage = 0.62% number of deletions = 31,788 mapped reads with deletion percentage = 1.6% homopolymer indels = 40.89% >>>>>>> Coverage mean coverageData = 0.0473X std coverageData = 0.3981X There is a 4.08% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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% 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 12191927 0.048914329485261344 0.5541317187370153 chr2 243199373 11646453 0.04788849928490564 0.6134942263728028 chr3 198022430 11813797 0.05965888308713311 0.28789038409363515 chr4 191154276 5812725 0.030408553350906992 0.20854817033506284 chr5 180915260 9952366 0.05501120248231133 0.27346483171626873 chr6 171115067 10154959 0.0593457909816907 0.29938001581434137 chr7 159138663 7429293 0.04668440000655277 0.5123200601912689 chr8 146364022 9829404 0.06715724168880792 0.5282919396347497 chr9 141213431 6392488 0.04526827196769973 0.380925907434601 chr10 135534747 7085242 0.05227620338568972 0.40545981487685406 chr11 135006516 6123152 0.045354492371316356 0.3326753903657599 chr12 133851895 5360269 0.04004626904983303 0.22433377454682413 chr13 115169878 4975232 0.04319907328546445 0.2309834657123322 chr14 107349540 3506215 0.03266166766993133 0.2353201668816896 chr15 102531392 2553471 0.02490428492378217 0.1756998718972374 chr16 90354753 3657024 0.040474063384357876 0.2598081091326329 chr17 81195210 4246410 0.05229877476762484 0.2893468083738622 chr18 78077248 4549113 0.058264259006669906 0.7692196024724115 chr19 59128983 2554426 0.043200912148277607 0.50132884744128 chr20 63025520 3498589 0.055510672502186414 0.29655679362418 chr21 48129895 3091212 0.06422644387651376 0.2998498466525592 chr22 51304566 2101959 0.04097021306056853 0.2302905010778025 chrMT 16571 173797 10.48802124192867 7.600733797444715 chrX 155270560 7341743 0.04728354814975872 0.31514892621275575 chrY 59373566 327096 0.00550911831706386 0.1532735660044635