BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038405.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 13,099,464 number of mapped reads = 12,739,628 (97.25%) number of supplementary alignments = 223,390 (1.71%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,444,328 number of mapped paired reads (second in pair) = 6,295,300 number of mapped paired reads (both in pair) = 12,575,320 number of mapped paired reads (singletons) = 164,308 number of mapped bases = 1,824,170,631 bp number of sequenced bases = 1,822,931,103 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,697,703 duplication rate = 8.18% >>>>>>> Insert size mean insert size = 89,658.7886 std insert size = 2,816,345.8806 median insert size = 266 >>>>>>> Mapping quality mean mapping quality = 53.8475 >>>>>>> ACTG content number of A's = 532,237,005 bp (29.2%) number of C's = 370,879,313 bp (20.35%) number of T's = 533,514,700 bp (29.27%) number of G's = 386,261,445 bp (21.19%) number of N's = 38,640 bp (0%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.014 number of mismatches = 24,753,856 number of insertions = 305,394 mapped reads with insertion percentage = 2.26% number of deletions = 611,864 mapped reads with deletion percentage = 4.62% homopolymer indels = 47.3% >>>>>>> Coverage mean coverageData = 0.5893X std coverageData = 8.0814X There is a 25.61% of reference with a coverageData >= 1X There is a 13.1% of reference with a coverageData >= 2X There is a 6.7% of reference with a coverageData >= 3X There is a 3.78% of reference with a coverageData >= 4X There is a 2.15% of reference with a coverageData >= 5X There is a 1.28% of reference with a coverageData >= 6X There is a 0.78% of reference with a coverageData >= 7X There is a 0.49% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 111055206 0.4455563863971276 7.182418063483421 chr2 243199373 156406512 0.6431205396240885 8.00700568228831 chr3 198022430 120786602 0.6099642449595231 1.3890580525128882 chr4 191154276 112157314 0.586737144190277 6.291568755941536 chr5 180915260 124227356 0.6866604619201276 1.5800470576563317 chr6 171115067 130391928 0.7620131311990195 9.82003290671791 chr7 159138663 129812618 0.8157201748012675 8.786118143986664 chr8 146364022 80749666 0.5517043389255865 2.0489841296723514 chr9 141213431 72507485 0.5134602600230003 10.743679186266435 chr10 135534747 79766374 0.5885308067900846 22.634968760303433 chr11 135006516 78649677 0.5825620816701914 3.539662430390778 chr12 133851895 63888953 0.4773107844308069 1.2003195193227245 chr13 115169878 123521101 1.0725122153902082 2.034991812294011 chr14 107349540 33689750 0.3138322716613411 1.0132893526308318 chr15 102531392 40727359 0.39721843433082427 1.0478434759800135 chr16 90354753 69728342 0.7717174767773423 16.722117728179562 chr17 81195210 39057452 0.4810314795663439 4.213596010498141 chr18 78077248 28420014 0.3639986645021095 8.984243832867065 chr19 59128983 20634371 0.34897219524306716 4.054817150360321 chr20 63025520 57102668 0.9060245437086437 2.4942165398945333 chr21 48129895 15651772 0.32519854863593617 3.0690452635444396 chr22 51304566 10447869 0.20364403823238655 0.817823841938379 chrMT 16571 7452993 449.7612093416209 197.17717135840934 chrX 155270560 91957002 0.5922372019525144 1.6436688467312952 chrY 59373566 25380247 0.4274671155847368 11.781032643808302