BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716660.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 = 639,777 number of mapped reads = 549,284 (85.86%) number of supplementary alignments = 2,187 (0.34%) number of secondary alignments = 0 number of mapped bases = 30,955,284 bp number of sequenced bases = 30,945,839 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,203 duplication rate = 1.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5803 >>>>>>> ACTG content number of A's = 7,329,965 bp (23.69%) number of C's = 5,935,305 bp (19.18%) number of T's = 9,761,989 bp (31.55%) number of G's = 7,918,067 bp (25.59%) number of N's = 513 bp (0%) GC percentage = 44.77% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 167,268 number of insertions = 2,232 mapped reads with insertion percentage = 0.4% number of deletions = 5,922 mapped reads with deletion percentage = 1.07% homopolymer indels = 40.89% >>>>>>> Coverage mean coverageData = 0.01X std coverageData = 0.1226X There is a 0.95% of reference with a coverageData >= 1X There is a 0.03% 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 2520211 0.010111152340920346 0.1481445946918349 chr2 243199373 2979292 0.012250409872561636 0.16469478558135586 chr3 198022430 2616047 0.013210862022044674 0.1240623402070864 chr4 191154276 1690325 0.008842726594303336 0.09969916371905164 chr5 180915260 1640758 0.009069207318387625 0.09849986979545496 chr6 171115067 1706137 0.009970700008550387 0.11003674044756448 chr7 159138663 1489131 0.009357443200336551 0.1491020775839903 chr8 146364022 2439658 0.01666842688977213 0.1432080601226816 chr9 141213431 1269934 0.008993011436709586 0.10323840165498752 chr10 135534747 1470633 0.01085059759620166 0.16231350467559386 chr11 135006516 1031668 0.007641616349836033 0.10041849415405096 chr12 133851895 1430220 0.010685093401180462 0.11259242173932581 chr13 115169878 788170 0.00684354289235246 0.08521262212764799 chr14 107349540 985644 0.009181632264097265 0.10001688431692278 chr15 102531392 720204 0.007024229223377754 0.08728158057509669 chr16 90354753 959862 0.010623259630846427 0.11220532767744733 chr17 81195210 1223640 0.015070347130083166 0.12986383102024113 chr18 78077248 656069 0.008402819218218347 0.12486940097565608 chr19 59128983 690258 0.011673767499096002 0.14955293594720726 chr20 63025520 697528 0.01106738984462167 0.11660932225546042 chr21 48129895 315240 0.006549775352719968 0.08621377568426486 chr22 51304566 477268 0.009302641796053786 0.0999696769940891 chrMT 16571 1251 0.07549333172409631 0.29278923322454786 chrX 155270560 1083753 0.006979771310156929 0.09552028751951029 chrY 59373566 72383 0.0012191115487319728 0.04528827272255104