The refseq entry tells you which non-refseq entry/entries it was derived from. In this case it says DQ386163, which suggests there are at least 2 pototo chloroplast sequences available - one by an Italian group and one by a Korean group.
On Thu, Apr 23, 2009 at 11:42 AM, Dan Bolser <[email protected]> wrote: > Hi, > > I found that the potato chloroplast sequence from GenBank (DQ231562.1) > has several differences (260 SNPs and 30 indels) relative to the same > sequence in RefSeq (NC_008096.1). As far as I am aware this sequence > has only been obtained once, why would the two differ? In general > should I trust the refseq sequence? > > > For your reference here is the output of dnadiff over the two files: > > Reference/DQ231562.fasta Query/NC_008096.fasta > NUCMER > > [REF] [QRY] > [Sequences] > TotalSeqs 1 1 > AlignedSeqs 1(100.00%) 1(100.00%) > UnalignedSeqs 0(0.00%) 0(0.00%) > > [Bases] > TotalBases 155312 155298 > AlignedBases 155312(100.00%) 155298(100.00%) > UnalignedBases 0(0.00%) 0(0.00%) > > [Alignments] > 1-to-1 1 1 > TotalLength 155312 155298 > AvgLength 155312.00 155298.00 > AvgIdentity 99.81 99.81 > > M-to-M 1 1 > TotalLength 155312 155298 > AvgLength 155312.00 155298.00 > AvgIdentity 99.81 99.81 > > [Feature Estimates] > Breakpoints 0 0 > Relocations 0 0 > Translocations 0 0 > Inversions 0 0 > > Insertions 0 0 > InsertionSum 0 0 > InsertionAvg 0.00 0.00 > > TandemIns 0 0 > TandemInsSum 0 0 > TandemInsAvg 0.00 0.00 > > [SNPs] > TotalSNPs 260 260 > AC 23(8.85%) 14(5.38%) > AG 24(9.23%) 30(11.54%) > AT 15(5.77%) 14(5.38%) > CA 14(5.38%) 23(8.85%) > CG 24(9.23%) 18(6.92%) > CT 32(12.31%) 19(7.31%) > GA 30(11.54%) 24(9.23%) > GC 18(6.92%) 24(9.23%) > GT 13(5.00%) 34(13.08%) > TA 14(5.38%) 15(5.77%) > TC 19(7.31%) 32(12.31%) > TG 34(13.08%) 13(5.00%) > > TotalGSNPs 113 113 > AC 9(7.96%) 8(7.08%) > AG 17(15.04%) 17(15.04%) > AT 5(4.42%) 3(2.65%) > CA 8(7.08%) 9(7.96%) > CG 6(5.31%) 7(6.19%) > CT 15(13.27%) 8(7.08%) > GA 17(15.04%) 17(15.04%) > GC 7(6.19%) 6(5.31%) > GT 6(5.31%) 12(10.62%) > TA 3(2.65%) 5(4.42%) > TC 8(7.08%) 15(13.27%) > TG 12(10.62%) 6(5.31%) > > TotalIndels 30 30 > A. 14(46.67%) 4(13.33%) > C. 1(3.33%) 0(0.00%) > G. 0(0.00%) 0(0.00%) > T. 7(23.33%) 4(13.33%) > > TotalGIndels 24 24 > A. 10(41.67%) 4(16.67%) > C. 1(4.17%) 0(0.00%) > G. 0(0.00%) 0(0.00%) > T. 5(20.83%) 4(16.67%) > > > Thanks for any pointers, > Dan. > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Ryan Raaum Assistant Professor Department of Anthropology Lehman College, The City University of New York 250 Bedford Park Blvd. West Bronx, NY 10468 e: [email protected] w: http://www.raaum.org o: (718) 960-8845 f: (718) 960-8406 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
