BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524780.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 = 1,322,867 number of mapped reads = 1,201,761 (90.85%) number of supplementary alignments = 4,090 (0.31%) number of secondary alignments = 0 number of mapped bases = 68,377,073 bp number of sequenced bases = 68,355,981 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,775 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4718 >>>>>>> ACTG content number of A's = 16,348,753 bp (23.92%) number of C's = 13,694,391 bp (20.03%) number of T's = 22,258,067 bp (32.56%) number of G's = 16,046,736 bp (23.48%) number of N's = 8,034 bp (0.01%) GC percentage = 43.51% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 346,644 number of insertions = 5,266 mapped reads with insertion percentage = 0.44% number of deletions = 13,239 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.12% >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 0.2105X There is a 2% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5435035 0.021805502342158656 0.2772618378243172 chr2 243199373 5803033 0.023861216944831516 0.3352488072922282 chr3 198022430 4470561 0.022576033432172304 0.16549635535031154 chr4 191154276 4367243 0.022846692689207748 0.18435926186534096 chr5 180915260 3982274 0.022011819235149097 0.16115521817371684 chr6 171115067 3924532 0.02293504639191124 0.18049683364350008 chr7 159138663 3741900 0.02351345631199629 0.24077852721204812 chr8 146364022 3448753 0.02356284661267371 0.19258599480112096 chr9 141213431 2894273 0.020495734573576077 0.18565126354606074 chr10 135534747 3327163 0.024548413404276322 0.24149714775479636 chr11 135006516 3107183 0.02301505951016468 0.19279843605333524 chr12 133851895 3095458 0.023125993098566142 0.16625290285303718 chr13 115169878 2133174 0.018521978463847986 0.1481509214616701 chr14 107349540 2008984 0.018714416475375674 0.15245555908638797 chr15 102531392 2002504 0.019530642868868884 0.15263508266465226 chr16 90354753 2106716 0.023316050678595733 0.1825715381064574 chr17 81195210 1894397 0.02333138863733464 0.17066674056902392 chr18 78077248 1809351 0.02317385725480488 0.2773315210397136 chr19 59128983 1516745 0.02565146435885765 0.23514681666378293 chr20 63025520 1495149 0.023722914146523503 0.1738517418331341 chr21 48129895 895982 0.018615914287783093 0.16098799161135446 chr22 51304566 873855 0.017032694516897384 0.1429307392699117 chrMT 16571 18838 1.136805262205057 1.2093965999115988 chrX 155270560 3794202 0.024436068241139853 0.18269873438206005 chrY 59373566 229768 0.0038698703055834644 0.11487433657178252