BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716868.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 = 521,609 number of mapped reads = 423,872 (81.26%) number of supplementary alignments = 1,309 (0.25%) number of secondary alignments = 0 number of mapped bases = 23,931,806 bp number of sequenced bases = 23,924,178 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,333 duplication rate = 1.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4551 >>>>>>> ACTG content number of A's = 5,655,009 bp (23.64%) number of C's = 4,725,431 bp (19.75%) number of T's = 7,819,454 bp (32.68%) number of G's = 5,723,865 bp (23.93%) number of N's = 419 bp (0%) GC percentage = 43.68% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 127,088 number of insertions = 1,953 mapped reads with insertion percentage = 0.46% number of deletions = 4,846 mapped reads with deletion percentage = 1.13% homopolymer indels = 37.84% >>>>>>> Coverage mean coverageData = 0.0077X std coverageData = 0.1006X There is a 0.74% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 1906625 0.007649429286677685 0.11153514278031221 chr2 243199373 2023008 0.008318310919329549 0.13563758387178335 chr3 198022430 1600997 0.008084927550884009 0.09246629571433848 chr4 191154276 1537347 0.008042441069955454 0.09624353544531705 chr5 180915260 1421877 0.007859353600133012 0.0909252102403309 chr6 171115067 1368392 0.00799691122465563 0.09571915602812167 chr7 159138663 1337193 0.008402690928727986 0.11516507714933312 chr8 146364022 1181233 0.008070514760792786 0.0975171370935363 chr9 141213431 993996 0.007038962179171187 0.09182663316180133 chr10 135534747 1161914 0.008572812697248773 0.10958659288006384 chr11 135006516 1069210 0.007919691816949043 0.09790706817695964 chr12 133851895 1085295 0.008108178072488252 0.0929662385119435 chr13 115169878 730161 0.006339860844517002 0.08177481692682273 chr14 107349540 727340 0.006775436578489297 0.08605789449606585 chr15 102531392 706563 0.006891187042501091 0.08531788629441779 chr16 90354753 722616 0.007997542752399533 0.09450007035604105 chr17 81195210 695742 0.008568756703751366 0.09700246142000368 chr18 78077248 620109 0.007942249706342108 0.11422587993684814 chr19 59128983 523828 0.008859073392146793 0.11086740132584492 chr20 63025520 511493 0.008115649025981856 0.09314083239533211 chr21 48129895 308957 0.006419232786607991 0.08510336666520393 chr22 51304566 305950 0.005963406843749541 0.07971401776314524 chrMT 16571 1492 0.09003681129684388 0.3384039502922771 chrX 155270560 1314274 0.008464412055962186 0.09766448723249889 chrY 59373566 76194 0.001283298362102758 0.04623152312161572