BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867858.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 = 3,025,163 number of mapped reads = 2,777,089 (91.8%) number of supplementary alignments = 12,505 (0.41%) number of secondary alignments = 0 number of mapped bases = 163,868,788 bp number of sequenced bases = 163,819,469 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 174,785 duplication rate = 4.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.788 >>>>>>> ACTG content number of A's = 41,074,562 bp (25.07%) number of C's = 33,363,806 bp (20.37%) number of T's = 52,476,694 bp (32.03%) number of G's = 36,882,658 bp (22.51%) number of N's = 21,749 bp (0.01%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 829,823 number of insertions = 11,607 mapped reads with insertion percentage = 0.42% number of deletions = 31,103 mapped reads with deletion percentage = 1.11% homopolymer indels = 44.01% >>>>>>> Coverage mean coverageData = 0.0529X std coverageData = 0.4718X There is a 4.47% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 13216924 0.05302664421445915 0.8934777038056714 chr2 243199373 13864490 0.05700874072565968 0.6699891478308324 chr3 198022430 10829497 0.05468823405510174 0.269314608385042 chr4 191154276 10532997 0.05510207367791239 0.3303185009284184 chr5 180915260 9875011 0.054583626610602114 0.2722302956972261 chr6 171115067 9310371 0.054410001195277564 0.32560851651069206 chr7 159138663 9089302 0.05711561118243151 0.567871020414215 chr8 146364022 8280092 0.056571908088177573 0.5229108106580925 chr9 141213431 6919369 0.04899936890563901 0.36923735459969853 chr10 135534747 8011737 0.05911205190798784 0.4676506380925489 chr11 135006516 7489713 0.05547667788123649 0.38858802851215457 chr12 133851895 7375180 0.05509955611760297 0.27643549597853484 chr13 115169878 5102712 0.04430595993164115 0.24584789454429812 chr14 107349540 4956130 0.0461681531192402 0.2639923322775027 chr15 102531392 4667172 0.045519444425371695 0.24620982117992463 chr16 90354753 4821508 0.053361974217338626 0.30071247767513654 chr17 81195210 4528451 0.05577239100680939 0.2941148739740687 chr18 78077248 4338539 0.0555672633338716 0.7476476384912869 chr19 59128983 3434892 0.0580915115688697 0.68649707921424 chr20 63025520 3462133 0.05493224014653112 0.28115976350250504 chr21 48129895 2127860 0.04421077585978527 0.29722297065785064 chr22 51304566 1949707 0.03800260195164695 0.2249962067666374 chrMT 16571 25964 1.5668336250075432 1.6155623121324063 chrX 155270560 9107861 0.05865800316557112 0.3248885440790965 chrY 59373566 551176 0.009283188414184185 0.3567837121916492