Assembly Information

[Overview] [RefSeq] [Assembly & SNP] [Alignment]

Assembly Name: 20110601C-000049

Sequence: [FASTA format sequence] CCTATGTTCG TAAATCGTTG ACTATACTCA ACAAACCACA AAGACATCGG CACCCTGTAC CTACTATTTG GTGCCTGAGC AGGAATAGTG GGCACTGCCT TGAGCCTACT AATTCGCGCT GAACTAGGTC AGCCCGGAAC CCTACTTGGC GATGATCAAA TCTATAATGT AATTGTTACA GCTCATGCCT TTGTAATAAT CTTCTTTATA GTAATACCCA TTATGATTGG GGGTTTTGGT AACTGACTCG TACCGCTAAT AATCGGAGCT CCCGATATGG CCTTTCCACG TATAAACAAC ATAAGTTTCT GACTACTTCC ACCATCCTTC CTATTACTTC TGGCATCCTC AATAGTAGAA GCCGGAGCGG GTACTGGATG AACTGTATAC CCACCTTTAG CTGGAAACTT AGCCCATGCA GGGGCTTCAG TTGATTTAAC AATTTTCTCC CTACACCTTG CAGGTGTATC ATCAATCCTA GGGGCTATTA ATTTCATTAC CACAATTATT AACATAAAAC CCCCCGCAAT GTCTCAATAC CAAACACCCC TGTTTGTCTG ATCAGTACTA ATCACAGCCG TACTACTTCT ACTATCCCTG CCAGTTCTAG CAGCTGGCAT TACTATACTA CTGACAGACC GCAACCTGAA CACAACCTTT TTTGATCCAG CAGGTGGCGG AGACCCTATC CTTTATCAAC ACTTGTTCTG ATTTTTCGGA CACCCAGAAG TATACATTCT CATCTTACCA GGATTCGGAA ATATCTCCCA CATTGTAACC TACTATTCAG GTAAAAAAGA ACATTTGGAT ATATAGGCAT AGTATGAGCC ATAATGTCCA TTGGAAATCT AGGTTTTTAT GTATGGGCCT CACACATATT CACCGTAGGA ATAGACGTAG ATACCCGAGC ATACTTTACA TCTGCTACAA TAATCATTGC TATTCCCACT GGAGTAAAAG TNATTAAGTG AATAGCTACC CTGCACGGCG GCAATATTAA ATGATCGCCC CCAAACTTNN GAGCTCTGGG CCTCATCTTC

SNP mapping information

SNP ID Rel. Chr. Location (cM)
Assembly Overview: TOP

Change score limit to

BLAST on RefSeq (Human): TOP

Locus Definition Score E value FL
COX1 cytochrome c oxidase subunit I [Homo sapiens]. 350 e-123 O

		Locus	Definition	Score	E value	FL
		COX1	cytochrome c oxidase subunit I [Homo sapiens].	350	e-123	O

BLAST on RefSeq (Mouse): TOP

Locus Definition Score E value FL
COX1 cytochrome c oxidase subunit I [Mus musculus]. 362 e-129 O

		Locus	Definition	Score	E value	FL
		COX1	cytochrome c oxidase subunit I [Mus musculus].	362	e-129	O

BLAST on RefSeq (Dog): TOP

Locus Definition Score E value FL
COX1 cytochrome c oxidase subunit I [Canis lupus familiaris]. 366 e-130 O

		Locus	Definition	Score	E value	FL
		COX1	cytochrome c oxidase subunit I [Canis lupus familiaris].	366	e-130	O

BLAST on RefSeq (Cattle): TOP

Locus Definition Score E value FL
COX1 cytochrome c oxidase subunit I [Bos taurus]. 362 e-129 O

LOC100301020 PREDICTED: cytochrome c oxidase subunit I-like, partial [Bos taurus]. 112 4e-25 O

LOC100299681 PREDICTED: cytochrome c oxidase subunit I-like [Bos taurus]. 95.5 7e-20 O

Locus	Definition	Score	E value	FL
COX1	cytochrome c oxidase subunit I [Bos taurus].	362	e-129	O
LOC100301020	PREDICTED: cytochrome c oxidase subunit I-like, partial [Bos taurus].	112	4e-25	O
LOC100299681	PREDICTED: cytochrome c oxidase subunit I-like [Bos taurus].	95.5	7e-20	O

BLAST on RefSeq (Pig): TOP

Locus Definition Score E value FL
COX1 cytochrome c oxidase subunit I [Sus scrofa]. 368 e-131 O

		Locus	Definition	Score	E value	FL
		COX1	cytochrome c oxidase subunit I [Sus scrofa].	368	e-131	O

Assembly Members: 4 TOP

Library Plate Loc. Read Name Accession Full Seq.

AMP01 0030 E06 AMP01_0030_E06.b BW957170
AMP01 0041 C08 AMP01_0041_C08.b BW957909
AMP01 0042 D04 AMP01_0042_D04.b BW957982
AMP01 0053 D08 AMP01_0053_D08.b BW958771

SNP: 1 TOP
Loc. Allele Individuals Freq. Type AA Change
Western Meishan
155 A 2 0 0.500 W N GAT/D
G 2 0 0.500 GGT/G

Alignment: TOP

20110601C-000049 : ............................................................
                   ---------+---------+---------+---------+---------+---------+ 0
AMP01_0042_D04.b : nnnggcgatanantaagggatacttgggggctgctcccgcaccgxxxxxxxxxxxxxxxx
AMP01_0030_E06.b : nnngggatatataaagggatacttxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
AMP01_0041_C08.b :   ngggatannttaagggatactaaxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
AMP01_0053_D08.b :       nnnggaaatnnnntttaacgaatcttgggctgctcgcccxxxxxxxxxxxxxxx


20110601C-000049 : ............................................................
                   ---------+---------+---------+---------+---------+---------+ 0
AMP01_0042_D04.b : xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
AMP01_0030_E06.b : xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
AMP01_0041_C08.b : xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
AMP01_0053_D08.b : xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx


20110601C-000049 : .................................................CCTATGTTCGT
                   ---------+---------+---------+---------+---------+---------+ 11
AMP01_0042_D04.b : xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxCCTATGTTCGT
AMP01_0030_E06.b : xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxCCTATGTTCGT
AMP01_0041_C08.b : xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxCCTATGTTCGT
AMP01_0053_D08.b : xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxTTCGT


20110601C-000049 : AAATCGTTGACTATACTCAACAAACCACAAAGACATCGGCACCCTGTACCTACTATTTGG
                   ---------+---------+---------+---------+---------+---------+ 71
AMP01_0042_D04.b : AAATCGTTGACTATACTCAACAAACCACAAAGACATCGGCACCCTGTACCTACTATTTGG
AMP01_0030_E06.b : AAATCGTTGACTATACTCAACAAACCACAAAGACATCGGCACCCTGTACCTACTATTTGG
AMP01_0041_C08.b : AAATCGTTGACTATACTCAACAAACCACAAAGACATCGGCACCCTGTACCTACTATTTGG
AMP01_0053_D08.b : AAATCGTTGACTATACTCAACAAACCACAAAGACATCGGCACCCTGTACCTACTATTTGG


20110601C-000049 : TGCCTGAGCAGGAATAGTGGGCACTGCCTTGAGCCTACTAATTCGCGCTGAACTAGGTCA
                   ---------+---------+---------+---------+---------+---------+ 131
AMP01_0042_D04.b : TGCCTGAGCAGGAATAGTGGGCACTGCCTTGAGCCTACTAATTCGCGCTGAACTAGGTCA
AMP01_0030_E06.b : TGCCTGAGCAGGAATAGTGGGCACTGCCTTGAGCCTACTAATTCGCGCTGAACTAGGTCA
AMP01_0041_C08.b : TGCCTGAGCAGGAATAGTGGGCACTGCCTTGAGCCTACTAATTCGCGCTGAACTAGGTCA
AMP01_0053_D08.b : TGCCTGAGCAGGAATAGTGGGCACTGCCTTGAGCCTACTAATTCGCGCTGAACTAGGTCA


20110601C-000049 : GCCCGGAACCCTACTTGGCGATGATCAAATCTATAATGTAATTGTTACAGCTCATGCCTT
                   ---------+---------+---------+---------+---------+---------+ 191
AMP01_0042_D04.b : GCCCGGAACCCTACTTGGCGATGGTCAAATCTATAATGTGATTGTTACAGCTCATGCCTT
AMP01_0030_E06.b : GCCCGGAACCCTACTTGGCGATGATCAAATCTATAATGTAATTGTTACAGCTCATGCCTT
AMP01_0041_C08.b : GCCCGGAACCCTACTTGGCGATGGTCAAATCTATAATGTAATTGTTACAGCTCATGCCTT
AMP01_0053_D08.b : GCCCGGAACCCTACTTGGCGATGATCAAATCTATAATGTAATTGTTACAGCTCATGCCTT


20110601C-000049 : TGTAATAATCTTCTTTATAGTAATACCCATTATGATTGGGGGTTTTGGTAACTGACTCGT
                   ---------+---------+---------+---------+---------+---------+ 251
AMP01_0042_D04.b : TGTAATAATCTTCTTTATAGTAATACCCATTATGATTGGGGGTTTTGGTAACCGACTCGT
AMP01_0030_E06.b : TGTAATAATCTTCTTTATAGTAATACCCATTATGATTGGGGGTTTTGGTAACTGACTCGT
AMP01_0041_C08.b : TGTAATAATCTTCTTTATAGTAATACCCATTATGATTGGGGGTTTTGGTAACTGACTCGT
AMP01_0053_D08.b : TGTAATAATCTTCTTTATAGTAATACCCATTATGATTGGGGGTTTTGGTAACTGACTCGT


20110601C-000049 : ACCGCTAATAATCGGAGCTCCCGATATGGCCTTTCCACGTATAAACAACATAAGTTTCTG
                   ---------+---------+---------+---------+---------+---------+ 311
AMP01_0042_D04.b : ACCGCTAATAATCGGAGCTCCCGATATGGCCTTTCCACGTATAAACAACATAAGTTTCTG
AMP01_0030_E06.b : ACCGCTAATAATCGGAGCTCCCGATATGGCCTTTCCACGTATAAACAACATAAGTTTCTG
AMP01_0041_C08.b : ACCGCTAATAATCGGAGCTCCCGATATGGCCTTTCCACGTATAAACAACATAAGTTTCTG
AMP01_0053_D08.b : ACCGCTAATAATCGGAGCTCCCGATATGGCCTTTCCACGTATAAACAACATAAGTTTCTG


20110601C-000049 : ACTACTTCCACCATCCTTCCTATTACTTCTGGCATCCTCAATAGTAGAAGCCGGAGCGGG
                   ---------+---------+---------+---------+---------+---------+ 371
AMP01_0042_D04.b : ACTACTTCCACCATCCTTCCTATTACTTCTGGCATCCTCAATAGTAGAAGCCGGAGCGGG
AMP01_0030_E06.b : ACTACTTCCACCATCCTTCCTATTACTTCTGGCATCCTCAATAGTAGAAGCCGGAGCGGG
AMP01_0041_C08.b : ACTACTTCCACCATCCTTCCTATTACTTCTGGCATCCTCAATAGTAGAAGCCGGAGCGGG
AMP01_0053_D08.b : ACTACTTCCACCATCCTTCCTATTACTTCTGGCATCCTCAATAGTAGAAGCCGGAGCGGG


20110601C-000049 : TACTGGATGAACTGTATACCCACCTTTAGCTGGAAACTTAGCCCATGCAGGGGCTTCAGT
                   ---------+---------+---------+---------+---------+---------+ 431
AMP01_0042_D04.b : TACTGGATGAACTGTATACCCACCTTTAGCTGGAAACTTAGCCCATGCAGGGGCTTCAGT
AMP01_0030_E06.b : TACTGGATGAACTGTATACCCACCTTTAGCTGGAAACTTAGCCCATGCAGGGGCTTCAGT
AMP01_0041_C08.b : TACTGGATGAACTGTATACCCACCTTTAGCTGGAAACTTAGCCCATGCAGGGGCTTCAGT
AMP01_0053_D08.b : TACTGGATGAACTGTATACCCACCTTTAGCTGGAAACTTAGCCCATGCAGGGGCTTCAGT


20110601C-000049 : TGATTTAACAATTTTCTCCCTACACCTTGCAGGTGTATCATCAATCCTAGGGGCTATTAA
                   ---------+---------+---------+---------+---------+---------+ 491
AMP01_0042_D04.b : TGATTTAACAATTTTCTCCCTACACCTTGCAGGTGTATCATCAATCCTAGGGGCTATTAA
AMP01_0030_E06.b : TGATTTAACAATTTTCTCCCTACACCTTGCAGGTGTATCATCAATCCTAGGGGCTATTAA
AMP01_0041_C08.b : TGATTTAACAATTTTCTCCCTACACCTTGCAGGTGTATCATCAATCCTAGGGGCTATTAA
AMP01_0053_D08.b : TGATTTAACAATTTTCTCCCTACACCTTGCAGGTGTATCATCAATCCTAGGGGCTATTAA


20110601C-000049 : TTTCATTACCACAATTATTAACATAAAACCCCCCGCAATGTCTCAATACCAAACACCCCT
                   ---------+---------+---------+---------+---------+---------+ 551
AMP01_0042_D04.b : TTTCATTACCACAATTATTAACATAAAACCCCCCGCAATGTCTCAATACCAAACACCCCT
AMP01_0030_E06.b : TTTCATTACCACAATTATTAACATAAAACCCCCCGCAATGTCTCAATACCAAACACCCCT
AMP01_0041_C08.b : TTTCATTACCACAATTATTAACATAAAACCCCCCGCAATGTCTCAATACCAAACACCCCT
AMP01_0053_D08.b : TTTCATTACCACAATTATTAACATAAAACCCCCCGCAATGTCTCAATACCAAACACCCCT


20110601C-000049 : GTTTGTCTGATCAGTACTAATCACAGCCGTACTACTTCTACTATCCCTGCCAGTTCTAGC
                   ---------+---------+---------+---------+---------+---------+ 611
AMP01_0042_D04.b : GTTTGTCTGATCAGTACTAATCACAGCCGTACTACTTCTACTATCCCTGCCAGTTCTAGC
AMP01_0030_E06.b : GTTTGTCTGATCAGTACTAATCACAGCCGTACTACTTCTACTATCCCTGCCAGTTCTAGC
AMP01_0041_C08.b : GTTTGTCTGATCAGTACTAATCACAGCCGTACTACTTCTACTATCCCTGCCAGTTCTAGC
AMP01_0053_D08.b : GTTTGTCTGATCAGTACTAATCACAGCCGTACTACTTCTACTATCCCTGCCAGTTCTAGC


20110601C-000049 : AGCTGGCATTACTATACTACTGACAGACCGCAACCTGAACACAACCTTTTTTGATCCAGC
                   ---------+---------+---------+---------+---------+---------+ 671
AMP01_0042_D04.b : AGCTGGCATTACTATACTACTGACAGACCGCAACCTGAACACAACCTTTTTTGATCCAGC
AMP01_0030_E06.b : AGCTGGCATTACTATACTACTGACAGACCGCAACCTGAACACAACCTTTTTTGATCCAGC
AMP01_0041_C08.b : AGCTGGCATTACTATACTACTGACAGACCGCAACCTGAACACAACCTTTTTTGATCCAGC
AMP01_0053_D08.b : AGCTGGCATTACTATACTACTGACAGACCGCAACCTGAACACAACCTTTTTTGATCCAGC


20110601C-000049 : AGGTGGCGGAGACCCTATCCTTTATCAACACTTGTTCTGATTTTTCGGACACCCAGAAGT
                   ---------+---------+---------+---------+---------+---------+ 731
AMP01_0042_D04.b : AGGTGGTGGAGACCCTATCCTTTATCAACACTTGTTCTGATTTTTCGGACACCCAGAAGT
AMP01_0030_E06.b : AGGTGGTGGAGACCCTATCCTTTATCAGCACTTGTTCTGATTTTTCGGACACCCAGAAGT
AMP01_0041_C08.b : AGGTGGCGGAGACCCTATCCTTTATCAACACTTGTTCTGATTTTTCGGACACCCAGAAGT
AMP01_0053_D08.b : ANGTGGTGGAGACCCTATCCTTTATCAACACTTGTTCTGATTTTTCGGACACCCAGAAGT


20110601C-000049 : ATACATTCTCATCTTACCAGGATTCGGAAATATCTCCCACATTGTAACCTACTATTCAGG
                   ---------+---------+---------+---------+---------+---------+ 791
AMP01_0042_D04.b : ATACATTCTCATCTTACCAGGATTCGGAAATATCTCCCACATTGTAACCTACTATTCAGG
AMP01_0030_E06.b : ATACATTCTCATCTTACCAGGATTCGGAATACTCTCCCACATTGTAACCTACTGATCANG
AMP01_0041_C08.b : ATACATTCTCATCTTACCAGGATTCGGAAATATCTCCCACATTGTAACCTACTAGTCANG
AMP01_0053_D08.b : ATACATTCTCATCTTACCAGGATTCGGAAATATCTCCCACATTTGTACCTACTNATCANG


20110601C-000049 : TAAAAAAG*AACATTTGGATATATAGGCATAGTATGAGCCATAATGTCCATTGGAAATCT
                   ---------+---------+---------+---------+---------+---------+ 850
AMP01_0042_D04.b : TAAAAAAG*AACATTTNGATATATAGGCATAGTATGAGCCATAATGTCCATTGGAATTCT
AMP01_0030_E06.b : TAAAAAAG*AACATTTGGATATATAGGCATAGTATGAGCCCATATGTCCATTTTGGATCT
AMP01_0041_C08.b : TAAAAAAGAAACATTTGGATATATAGGCATAGTATGAGCCATAATGTCCATTGGNAATCT
AMP01_0053_D08.b : TAAAAAAG*AACATTTGGATATATAGGCATAGTATGAGCCATAATGTCCATTGGATTTCT


20110601C-000049 : AGGTTTTTATGTATGGGCCTCACACATATTCACCGTAGGAA*TAGACGTAGATACCCGAG
                   ---------+---------+---------+---------+---------+---------+ 909
AMP01_0042_D04.b : ANNG*TTTATGTATGGG*CTCACACATNATCACGTANGAtagacgtagatcccgagcata
AMP01_0030_E06.b : NANGTTTTATGTATGGGNCTCACACATATTCACCGTAGGAA*TAGACGTAGATACCCGAG
AMP01_0041_C08.b : ANNNGTTTATGTATGGGNCTCACACATATTCACCGTAGGAA*TAGACGTAGATACCCGAG
AMP01_0053_D08.b : AGGTTTTTATGTATGGGCTCACCACATATTCACCGTAGGAAATAGACGTAGATACCCGAG


20110601C-000049 : CATACTTTACATCTGCTACAATAATCATTGCTATTCCCACTGGAGTAAAAGTNATTAAGT
                   ---------+---------+---------+---------+---------+---------+ 969
AMP01_0042_D04.b : ctttactctgctacataatcatgctattccactggagtaaagtattagttgatagctacc
AMP01_0030_E06.b : CATACTTTACATCTGCTACAATAATCATTGC*TATCCCACTGGAGTAAAagttttagttg
AMP01_0041_C08.b : CATACTTTACATCTGCTACNATAATCATTGCCTATCCCACTGGNATAAAAGTNATTAAGT
AMP01_0053_D08.b : CATACTTTACATCTGCTACAATAATCATTGCTATTCCCACTGGAtaaaagttattaggtg


20110601C-000049 : GAATAGCTACCCTGCACGGCGGCAATATTAAATGATCGCCCCCAAACTTNNGAGCTCTGG
                   ---------+---------+---------+---------+---------+---------+ 1029
AMP01_0042_D04.b : cctgcacgcgcataataatgatcgccgcatacttggactctgcttctcttctatcaccgt
AMP01_0030_E06.b : aatacctaccctgccggccgcaatattaatgatccccgcaaactatgactctggcctcat
AMP01_0041_C08.b : GAATAGCTACCCTGCACGGCGGCAATATTAAATGATCGCCCCCAAACTTNNGAGCTCTGG
AMP01_0053_D08.b : aatagctccctggccggggggcataattaatgatcgcccccatactatgagctctgggct


20110601C-000049 : GCCTCATCTTC.................................................
                   ---------+---------+---------+---------+---------+---------+ 1040
AMP01_0042_D04.b : agagtctacggcatgnactactatcccctaaaactgatactgaacaattaggacccacat
AMP01_0030_E06.b : ctcctatccccgtagaggtctacgggcatggactaccaatccccctaacatgaatacctg
AMP01_0041_C08.b : GCCTCATCTTCtattcaccgtagaggtctaaggggcatgtaaaacctattccccccaaac
AMP01_0053_D08.b : tcatcttctantccccgtaagaggtttaaggggcatttgataacaattcccccccaaatg


20110601C-000049 : ............................................................
                   ---------+---------+---------+---------+---------+---------+ 1040
AMP01_0042_D04.b : cctattcttacaaggaacggttccctaagggcttttcgattccttttcgggcccccacgg
AMP01_0030_E06.b : taacatttggacccccaatccctatttttaccaagaacatgttccaatagaggggttgtt
AMP01_0041_C08.b : atgnatacaggaaacattttgtagcccccactcccatttttaataaagaaaagtttccat
AMP01_0053_D08.b : tgttaa                                                     


20110601C-000049 : ............................................................
                   ---------+---------+---------+---------+---------+---------+ 1040
AMP01_0042_D04.b : gaaattctttttaataaggaataacctctcacttggaccaaccaccaccgca       
AMP01_0030_E06.b : cccaatcccgtttcggggcccctcccccatggcaaattcttttaagatggagaaatttac
AMP01_0041_C08.b : aaaggggtttgtttcaatccccttttccgggaccnnacaaaggaaaatttctttttattt
AMP01_0053_D08.b :                                                             


20110601C-000049 : ............................................................
                   ---------+---------+---------+---------+---------+---------+ 1040
AMP01_0042_D04.b :                                                             
AMP01_0030_E06.b : tcttccca                                                   
AMP01_0041_C08.b : ttagaaaaa                                                  
AMP01_0053_D08.b :