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| Status |
Public on Feb 11, 2019 |
| Title |
[Pf_SNP_2_geno_pm] Affymetrix Plasmodium falciparum 75K SNP |
| Technology type |
in situ oligonucleotide |
| Distribution |
custom-commercial |
| Organism |
Plasmodium falciparum |
| Manufacturer |
Affymetrix |
| Manufacture protocol |
Affymetrix protocols; see web site (www.affymetrix.com) for details.
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| Description |
Affymetrix-Pf-75k-SNP
Pf_SNP 2m520607 49 format
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| |
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| Submission date |
Feb 25, 2016 |
| Last update date |
Feb 11, 2019 |
| Contact name |
Dan Sturdevant |
| E-mail(s) |
dsturdevant@niaid.nih.gov
|
| Phone |
4063639248
|
| Organization name |
NIH
|
| Department |
NIAID
|
| Lab |
RTS
|
| Street address |
903 S 4th street
|
| City |
Hamilton |
| State/province |
MT |
| ZIP/Postal code |
59840 |
| Country |
USA |
| |
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| Samples (57)
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GSM2072646, GSM2072647, GSM2072648, GSM2072649, GSM2072650, GSM2072651
GSM2072652, GSM2072653, GSM2072654, GSM2072655, GSM2072656, GSM2072657, GSM2072658, GSM2072659, GSM2072660, GSM2072661, GSM2072662, GSM2072663, GSM2072664, GSM2072665, GSM2072666, GSM2072667, GSM2072668, GSM2072669, GSM2072670, GSM2072671, GSM2072672, GSM2072673, GSM2072674, GSM2072675, GSM2072676, GSM2072677, GSM2072678, GSM2072679, GSM2072680, GSM2072681, GSM2072682, GSM2072683, GSM2072684, GSM2072685, GSM2072686, GSM2072687, GSM2072688, GSM2072689, GSM2072690, GSM2072691, GSM2072692, GSM2072693, GSM2072694, GSM2072695, GSM2072696, GSM2072697, GSM2072698, GSM2072699, GSM2072700, GSM2072701, GSM2072702
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| Series (1) |
| GSE78689 |
K13 580Y allele not linked to increased P. falciparum recrudescences in artesunate-treated Aotus |
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| Data table header descriptions |
| ID |
|
| Location |
Location within reference strain 3D7 from plasmoDB |
| Chromosome |
Chromosome from plasmoDB |
| Position |
bp location within reference strain 3D7 from plasmoDB |
| Strains |
Strains that have this SNP |
| Left_Flank |
Sequence from left |
| Reference_Allele |
SNP of interrogation |
| Right_Flank |
Sequence from right |
| Major_Allele_Frequency |
Frequency of major allele |
| Minor_Allele_Frequency |
Frequency of minor allele |
| Major_Allele |
Major allele (A) |
| Minor_Allele |
Minor allele (B) |
| Gene_ID |
Gene identification from plasmoDB |
| SPOT_ID |
|
| Data table |
| ID |
Location |
Chromosome |
Position |
Strains |
Left_Flank |
Reference_Allele |
Right_Flank |
Major_Allele_Frequency |
Minor_Allele_Frequency |
Major_Allele |
Minor_Allele |
Gene_ID |
SPOT_ID |
| Pf_01_000001449 |
Pf3D7_01_v3: 1226 |
1 |
1226 |
HB3:A, V1_S:A, Senegal3404:A, 3D7:A, 7G8:C, 3D7:A |
ACTTACTCTTATATTCTTTTTATCATGTTCAAGGTCTTACTTCTTAAATATTAGGTCCTT |
A |
ATCTCATAATTCTACTCTTACTTTCTTACTTCTAGAACCTTATTCTTACTTTCTTCATCT |
0.83 |
0.17 |
A |
C |
null |
Pf_01_000001449 |
| Pf_01_000001634 |
Pf3D7_01_v3: 1411 |
1 |
1411 |
3D7:C, Senegal3404:C, V1_S:C, HB3:C, 3D7:C, 7G8:C, Dd2:G |
TACTTCTCATTTCTTACTCTTACATACCTTCTCTTCATTCTTCAATCATCAATTCTCACT |
C |
TTCATTCCTTGGTCTTACTTCTTTCTTCTTAATGTCATACTTTTATCCCCTATTATCATC |
0.86 |
0.14 |
C |
G |
null |
Pf_01_000001634 |
| Pf_01_000001635 |
Pf3D7_01_v3: 1412 |
1 |
1412 |
Dd2:T, 3D7:T, Senegal3404:A, 3D7:T, HB3:T, V1_S:A, 7G8:A |
ACTTCTCATTTCTTACTCTTACATACCTTCTCTTCATTCTTCAATCATCAATTCTCACTC |
T |
TCATTCCTTGGTCTTACTTCTTTCTTCTTAATGTCATACTTTTATCCCCTATTATCATCT |
0.57 |
0.43 |
T |
A |
null |
Pf_01_000001635 |
| Pf_01_000001637 |
Pf3D7_01_v3: 1414 |
1 |
1414 |
Dd2:C, HB3:T, 3D7:C, 3D7:C, 7G8:C |
TTCTCATTTCTTACTCTTACATACCTTCTCTTCATTCTTCAATCATCAATTCTCACTCTT |
C |
ATTCCTTGGTCTTACTTCTTTCTTCTTAATGTCATACTTTTATCCCCTATTATCATCTAC |
0.8 |
0.2 |
C |
T |
null |
Pf_01_000001637 |
| Pf_01_000001646 |
Pf3D7_01_v3: 1423 |
1 |
1423 |
HB3:A, 3D7:G, 3D7:G, 7G8:G, Dd2:A |
CTTACTCTTACATACCTTCTCTTCATTCTTCAATCATCAATTCTCACTCTTCATTCCTTG |
G |
TCTTACTTCTTTCTTCTTAATGTCATACTTTTATCCCCTATTATCATCTACTTAGTCTTC |
0.6 |
0.4 |
G |
A |
null |
Pf_01_000001646 |
| Pf_01_000001717 |
Pf3D7_01_v3: 1494 |
1 |
1494 |
V1_S:C, 3D7:C, HB3:C, 3D7:C, 7G8:G, Senegal3404:C, Dd2:C |
TTCTTCTTAATGTCATACTTTTATCCCCTATTATCATCTACTTAGTCTTCATTTACTCTT |
C |
TAACTTCTTCATCTATCACTTTTCATCATCATTCATGCTTACTTAACTTACTTTCATATA |
0.86 |
0.14 |
C |
G |
null |
Pf_01_000001717 |
| Pf_01_000001733 |
Pf3D7_01_v3: 1510 |
1 |
1510 |
V1_S:T, 7G8:C, Dd2:T, 3D7:T, HB3:T, 3D7:T |
ACTTTTATCCCCTATTATCATCTACTTAGTCTTCATTTACTCTTCTAACTTCTTCATCTA |
T |
CACTTTTCATCATCATTCATGCTTACTTAACTTACTTTCATATACTTACTTCTACTACAT |
0.83 |
0.17 |
T |
C |
null |
Pf_01_000001733 |
| Pf_01_000001745 |
Pf3D7_01_v3: 1522 |
1 |
1522 |
HB3:A, 3D7:A, V1_S:A, 7G8:A, Dd2:C, 3D7:A, Senegal3404:A |
TATTATCATCTACTTAGTCTTCATTTACTCTTCTAACTTCTTCATCTATCACTTTTCATC |
A |
TCATTCATGCTTACTTAACTTACTTTCATATACTTACTTCTACTACATCTTCACCAAATC |
0.86 |
0.14 |
A |
C |
null |
Pf_01_000001745 |
| Pf_01_000001762 |
Pf3D7_01_v3: 1539 |
1 |
1539 |
3D7:A, V1_S:T, 3D7:A, Dd2:A, HB3:A, 7G8:A |
TCTTCATTTACTCTTCTAACTTCTTCATCTATCACTTTTCATCATCATTCATGCTTACTT |
A |
ACTTACTTTCATATACTTACTTCTACTACATCTTCACCAAATCCGGACTTAGCTTAACTT |
0.83 |
0.17 |
A |
T |
null |
Pf_01_000001762 |
| Pf_01_000001763 |
Pf3D7_01_v3: 1540 |
1 |
1540 |
3D7:A, V1_S:T, Dd2:A, HB3:A, 7G8:A, 3D7:A |
CTTCATTTACTCTTCTAACTTCTTCATCTATCACTTTTCATCATCATTCATGCTTACTTA |
A |
CTTACTTTCATATACTTACTTCTACTACATCTTCACCAAATCCGGACTTAGCTTAACTTT |
0.83 |
0.17 |
A |
T |
null |
Pf_01_000001763 |
| Pf_01_000001785 |
Pf3D7_01_v3: 1562 |
1 |
1562 |
3D7:C, 7G8:C, V1_S:G, 3D7:C, Dd2:C, HB3:C |
TTCATCTATCACTTTTCATCATCATTCATGCTTACTTAACTTACTTTCATATACTTACTT |
C |
TACTACATCTTCACCAAATCCGGACTTAGCTTAACTTTTCTCTCTTTATTCTTACCTTAC |
0.83 |
0.17 |
C |
G |
null |
Pf_01_000001785 |
| Pf_01_000001808 |
Pf3D7_01_v3: 1585 |
1 |
1585 |
Dd2:C, HB3:C, V1_S:G, 3D7:G, 7G8:G, 3D7:G |
ATTCATGCTTACTTAACTTACTTTCATATACTTACTTCTACTACATCTTCACCAAATCCG |
G |
ACTTAGCTTAACTTTTCTCTCTTTATTCTTACCTTACTTAGCTCTTACATACTTAGGATC |
0.67 |
0.33 |
G |
C |
null |
Pf_01_000001808 |
| Pf_01_000001814 |
Pf3D7_01_v3: 1591 |
1 |
1591 |
HB3:G, 3D7:G, 7G8:C, V1_S:C, 3D7:G |
GCTTACTTAACTTACTTTCATATACTTACTTCTACTACATCTTCACCAAATCCGGACTTA |
G |
CTTAACTTTTCTCTCTTTATTCTTACCTTACTTAGCTCTTACATACTTAGGATCTACTTC |
0.6 |
0.4 |
G |
C |
null |
Pf_01_000001814 |
| Pf_01_000002004 |
Pf3D7_01_v3: 1781 |
1 |
1781 |
HB3:C, Senegal3404:C, Dd2:C, V1_S:C, 3D7:T, 7G8:T, D10:C, 3D7:T |
TATCTTACTTCTTTATTCTCAGATTCCGGACTTAGCTTAACTTTTTTGTGTTTGTTCTTA |
T |
CTTACTTAGCTCTTACATACTTAGGATCTACTTCTTTACTTACTTTCTTCTTACTTATGT |
0.63 |
0.38 |
C |
T |
null |
Pf_01_000002004 |
| Pf_01_000002013 |
Pf3D7_01_v3: 1790 |
1 |
1790 |
HB3:G, Dd2:C, 7G8:G, V1_S:C, 3D7:G, 3D7:G, Senegal3404:C |
TCTTTATTCTCAGATTCCGGACTTAGCTTAACTTTTTTGTGTTTGTTCTTATCTTACTTA |
G |
CTCTTACATACTTAGGATCTACTTCTTTACTTACTTTCTTCTTACTTATGTGGTAATAAG |
0.57 |
0.43 |
G |
C |
null |
Pf_01_000002013 |
| Pf_01_000002073 |
Pf3D7_01_v3: 1850 |
1 |
1850 |
3D7:G, Senegal3404:A, Dd2:G, 3D7:G |
GCTCTTACATACTTAGGATCTACTTCTTTACTTACTTTCTTCTTACTTATGTGGTAATAA |
G |
CTACTCGGTTGGGCACTAAGGTTAGGTTTAGCTGTTCTTTAGTTCTTAAAGGGTAAGAAT |
0.75 |
0.25 |
G |
A |
null |
Pf_01_000002073 |
| Pf_01_000002074 |
Pf3D7_01_v3: 1851 |
1 |
1851 |
3D7:C, 3D7:C, Senegal3404:G, Dd2:C |
CTCTTACATACTTAGGATCTACTTCTTTACTTACTTTCTTCTTACTTATGTGGTAATAAG |
C |
TACTCGGTTGGGCACTAAGGTTAGGTTTAGCTGTTCTTTAGTTCTTAAAGGGTAAGAATT |
0.75 |
0.25 |
C |
G |
null |
Pf_01_000002074 |
| Pf_01_000002133 |
Pf3D7_01_v3: 1910 |
1 |
1910 |
HB3:T, Dd2:A, Senegal3404:T, 3D7:T, 3D7:T, V1_S:T |
GCTACTCGGTTGGGCACTAAGGTTAGGTTTAGCTGTTCTTTAGTTCTTAAAGGGTAAGAA |
T |
TTAAGGTTTGTATTGAATTATTATTACTATTTCATTACTATTGTTGCTATTAAGGACTTA |
0.83 |
0.17 |
T |
A |
null |
Pf_01_000002133 |
| Pf_01_000002136 |
Pf3D7_01_v3: 1913 |
1 |
1913 |
3D7:A, 3D7:A, HB3:T, V1_S:A, Senegal3404:A |
ACTCGGTTGGGCACTAAGGTTAGGTTTAGCTGTTCTTTAGTTCTTAAAGGGTAAGAATTT |
A |
AGGTTTGTATTGAATTATTATTACTATTTCATTACTATTGTTGCTATTAAGGACTTATAA |
0.8 |
0.2 |
A |
T |
null |
Pf_01_000002136 |
| Pf_01_000002138 |
Pf3D7_01_v3: 1915 |
1 |
1915 |
V1_S:G, 3D7:G, Senegal3404:T, 3D7:G |
TCGGTTGGGCACTAAGGTTAGGTTTAGCTGTTCTTTAGTTCTTAAAGGGTAAGAATTTAA |
G |
GTTTGTATTGAATTATTATTACTATTTCATTACTATTGTTGCTATTAAGGACTTATAATG |
0.75 |
0.25 |
G |
T |
null |
Pf_01_000002138 |
Total number of rows: 76184
Table truncated, full table size 17845 Kbytes.
| Supplementary file |
Size |
Download |
File type/resource |
| GPL21519_Pf_SNP_2_geno_pm.CDF.gz |
54.0 Mb |
(ftp)(http) |
CDF |
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