BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238544.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 = 4,231,941 number of mapped reads = 3,853,274 (91.05%) number of supplementary alignments = 33,671 (0.8%) number of secondary alignments = 0 number of mapped bases = 239,669,136 bp number of sequenced bases = 239,533,977 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 843,605 duplication rate = 17.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2165 >>>>>>> ACTG content number of A's = 59,983,189 bp (25.04%) number of C's = 42,723,307 bp (17.84%) number of T's = 79,604,269 bp (33.23%) number of G's = 57,206,282 bp (23.88%) number of N's = 16,930 bp (0.01%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,423,518 number of insertions = 15,480 mapped reads with insertion percentage = 0.4% number of deletions = 79,991 mapped reads with deletion percentage = 2.05% homopolymer indels = 40.93% >>>>>>> Coverage mean coverageData = 0.0774X std coverageData = 0.9826X There is a 4.31% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 20430594 0.08196807662116115 0.822045623366017 chr2 243199373 19003831 0.0781409539242521 2.5339464344566682 chr3 198022430 10383663 0.05243680223497914 0.39481910589198155 chr4 191154276 9743151 0.05097009182258628 0.37325345562380996 chr5 180915260 8714581 0.048169408152745105 0.37405292186789857 chr6 171115067 15554562 0.09090118288648422 0.9192933993167193 chr7 159138663 20518186 0.12893275344408292 1.3099482682232761 chr8 146364022 17195604 0.11748518361978329 0.8797698646340106 chr9 141213431 6027988 0.04268707273318782 0.44800367032266325 chr10 135534747 11555415 0.08525795233896737 0.5115699931762147 chr11 135006516 5363219 0.03972563072437185 0.3430279987665015 chr12 133851895 6267005 0.046820442848418395 0.3655422776795892 chr13 115169878 10042704 0.08719905043226667 0.6749176188269049 chr14 107349540 6675163 0.062181570596390075 0.42318563336601667 chr15 102531392 4637191 0.045227036418270805 0.6002112877603893 chr16 90354753 11060211 0.12240873482328041 0.6234187266863317 chr17 81195210 7557867 0.09308267076346007 0.5044108245837611 chr18 78077248 12478652 0.15982443438580213 1.8076127374914677 chr19 59128983 6025086 0.1018973385691413 0.7121151581500262 chr20 63025520 7364070 0.11684266944564678 0.585759023054493 chr21 48129895 4927555 0.1023803397036291 0.5445332323904056 chr22 51304566 2743700 0.05347867088477076 0.37223049912234524 chrMT 16571 40748 2.458994629171444 3.0657344082866307 chrX 155270560 14806802 0.09536129708039953 0.5380200879777144 chrY 59373566 551588 0.009290127529143188 0.3468527219317905