BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068066.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,957,652 number of mapped reads = 3,662,212 (92.53%) number of supplementary alignments = 30,784 (0.78%) number of secondary alignments = 0 number of mapped bases = 236,256,774 bp number of sequenced bases = 236,167,733 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 627,168 duplication rate = 13.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7493 >>>>>>> ACTG content number of A's = 61,558,496 bp (26.07%) number of C's = 42,311,962 bp (17.92%) number of T's = 77,249,506 bp (32.71%) number of G's = 55,021,048 bp (23.3%) number of N's = 26,721 bp (0.01%) GC percentage = 41.21% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,264,353 number of insertions = 15,546 mapped reads with insertion percentage = 0.42% number of deletions = 51,721 mapped reads with deletion percentage = 1.4% homopolymer indels = 45.09% >>>>>>> Coverage mean coverageData = 0.0763X std coverageData = 0.879X There is a 4.93% of reference with a coverageData >= 1X There is a 1.61% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 24214798 0.09715040188405388 1.723119234991784 chr2 243199373 22369024 0.09197813186796333 1.5805554822638077 chr3 198022430 14909875 0.0752938694874111 0.3984338218419605 chr4 191154276 12262962 0.06415217203930086 0.406313869735593 chr5 180915260 11114212 0.06143324780894657 0.3603527290423157 chr6 171115067 17139581 0.10016406679138314 0.6295751291113133 chr7 159138663 19905888 0.12508517807517336 1.2465416498155664 chr8 146364022 8861112 0.060541599492257736 0.9888492070921587 chr9 141213431 7877508 0.05578441047863216 0.5946141642892113 chr10 135534747 12279460 0.09060008796120747 0.5656891467117297 chr11 135006516 11494140 0.08513766846631314 0.5669747783225525 chr12 133851895 9259512 0.0691772948003463 0.40652004953189647 chr13 115169878 5772286 0.0501197544031435 0.3820119006397884 chr14 107349540 5061337 0.047148194580060615 0.3741927216897003 chr15 102531392 4507164 0.043958868714081244 0.33677643410098956 chr16 90354753 4949796 0.054781799912617765 0.3714483557496462 chr17 81195210 6856648 0.08444645934162864 0.45034334087235756 chr18 78077248 5038573 0.06453317873088969 1.1782764104388608 chr19 59128983 4435804 0.07501911541417852 1.1295534189176741 chr20 63025520 3921921 0.06222750720660456 0.383560068054776 chr21 48129895 4685809 0.09735755708588187 0.46793451311940515 chr22 51304566 2576844 0.050226406749060114 0.3167229027374114 chrMT 16571 213434 12.87997103373363 8.915013958674574 chrX 155270560 15875207 0.10224222157761265 0.5560150987742459 chrY 59373566 673879 0.011349815168588661 0.3157949192788697