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Table 2 DNA sequencing verification of false negative (Fn) and false positive (Fp) calls

From: Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray

Gene ID

Chr position

Mism alle

SFPn

3D7

7G8

Forward (5'-3')

Reversed (5'-3')

MAL2.808

chr2: 306218

T/A

Fn(0/5)

A

A

tcagtagtatcttttgtttc

atgtaaaactaccatcaaatg

PFC0210c

chr3: 218122

G/G

Fp(4/0)

C

C

agatgtgttctttatctaatt

aaccaagtgataagcacata

PFC0235w

chr3: 248155

A/G

Fn(0/2)

A

A

ggaaatgtatttgagaaaaac

caatgtttactatccgaatt

PFC0770c

chr3: 718081

T/T

Fp(4/0)

T

A

atggggagcaaagaatttc

tattccatgatgtattatgat

PFC1065w

chr3: 995530

C/G

Fn(1/8)

G

G

ggaaaaagaagaagatttaa

aatatatcttccgaatcatc

PFC1065w

chr3: 995640

A/G

Fn(0/8)

A

A

atagatgtatcgtgtgataa

attattacttctgtctctag

PFE1390w

chr5: 1154254

A/A

Fp(3/0)

T

T

cgaaaaagagaagaaaaact

tgtgttggcttcttaatatt

MAL6P1.232

chr6: 817214

T/A

Fn(0/4)

T

T

tccaaatcttctcaaagct

ggtttattcaaaacattagg

MAL7.743

chr7: 181822

C/C

Fp(5/0)

C

G

tttaatgcttccctttgctt

ataattgtgatgaagtgatg

MAL7P1.30

chr7: 512599

T/T

Fp(1/0)

A

A

atggtagaataattcatatgt

ttatcacacatggtttcaac

MAL7P1.65

chr7: 519234

T/C

Fn(0/2)

T

C

aaaacaaccgtctgatataa

taaacaataaatccaactgt

MAL7.2803

chr7: 621749

G/A

Fn(0/6)

G

G

ttttcgctcggattattaaa

gcaacatgatttttttttttc

MAL7P1.67

chr7: 677205

C/A

Fn(0/2)

G

T

atttaacttactggattggt

aatggacaaccaggttaaaa

MAL7P1.82

chr7: 794419

A/C

Fn(0/7)

A

A

gtgtacttcattttgtagtta

atatctacaaaaggggaatt

MAL7P1.82

chr7: 794421

C/A

Fn(0/7)

A

A

ccatgtgctttcatatatat

ccatgtaccagctcatac

PF07_0102

chr7: 922368

C/A

Fn(0/4)

C

C

aagagtattaataattccgtc

gaacagaggatgaattattt

MAL8P1.42

chr8: 1017925

T/A

Fn(0/1)

T

A

tccatgatatattcccaag

tattcctcatttcagggtat

MAL8.3159

chr8: 1057901

C/A

Fn(0/3)

C

C

gtacagctagttgtagtg

gagctttcttactaaagtat

PF08_0017

chr8: 1179041

C/T

Fn(0/1)

C

T

cggtgataataataaatacg

gaatttatagaactttccgc

PF08_0017

chr8: 169329

T/C

Fn(0/1)

T

T

ccgtctacacaataattcttt

gggtagtaaatatgaggaaa

MAL8.2086

chr8: 582828

T/C

Fn(0/4)

T

T

tgggataaacctatgtataa

tcattcaaatttacaggtcg

PFI1300c

chr9: 1080645

T/T

Fp(1/0)

A

A

tatgatgacaatcatattcc

ccttctatgaatagagatac

PFI1300c

chr9: 1080729

G/A

Fn(0/2)

T

C

tacccatatcttgatttacg

ctttggagatttgtttagat

PFI0495w

chr9: 464714

G/G

Fp(5/0)

G

A

attctcccaaaactgaaata

atatcttcgttagttatgtg

MAL9.1104

chr9: 548591

A/G

Fn(0/1)

A

G

tcttcttttcctttctacat

ttaaggttccttctgaatta

PFI0690c

chr9: 603205

T/A

Fn(0/2)

T

T

cgaaaaaatcctttacctt

aaagatttccccctactaaa

MAL5.878

chr9: 926274

G/A

Fn(0/1)

C

C

gttcgtcttttttttcatatg

Gaatataagacagatgttcc

PF10_0314

chr10: 1294935

C/G

Fn(3/17)

T

T

caatgtgaggaatatttatag

ggcctcattgtggttatta

MAL10.3336

chr10: 1334877

A/A

Fp(1/0)

A

A

tttaaacacccctcaaaaaa

aaatatcaaaaccggaaatg

MAL10.4084

chr10: 1433239

G/A

Fn(0/1)

C

C

aagaaataattggttgggct

ttctgtccaccatttttttg

PF10_0377

chr10: 1554669

T/A

Fn(9/11)

T

A

taaaacctgtataaccaaata

tatacaaactttacaaaactc

PF10_0094

chr10: 389999

A/C

Fn(0/2)

T

T

aaggtataccaatagatttg

gtaaatcattcaccctcat

PF10_0138

chr10: 556132

C/C

Fp(2/1)

C

C

taatgtgtatgtatcagcta

ggattgtaataagtatatgg

MAL10.1222

chr10: 564556

T/T

Fp(1/0)

T

T

gttttatgcttaggcttata

tgggaaaatataaatgaagg

PF11_0338

chr11: 1272493

A/A

Fp(1/0)

A

A

gaatgttaacatacaaatgta

cttcagggagaatatttattc

MAL11.3013

chr11: 1294419

T/T

Fp(3/0)

T

T

tcatggttcaggtataaga

ccattattttcttgagctgc

PF11_0353

chr11: 1327608

G/A

Fn(0/5)

G

G

ttataccatatgtgtacaaag

gaaatatcaaaatttcctaac

PF11_0360

chr11: 1369690

A/G

Fn(0/3)

A

A

cctattctattcaatactgt

ctgtatacatttgtttggat

PF11_0046

chr11: 151916

A/G

Fn(0/2)

A

A

acaagcatagatatcatagc

ataacatgtcctaaaggtga

PF11_0441

chr11: 1717528

T/A

Fn(5/15)

A

T

cagttatatacctttatcag

ataagaaaaaatatccacac

MAL12.4052

chr12: 1192527

T/G

Fn(1/2)

T

G

ggatattcacaatggatttt

catgtgtatcatttatacatg

MAL12.2128

chr12: 577914

T/T

Fp(1/0)

T

T

ctgatgaaagaatacatattg

tgaacaatatattcggaaac

MAL12.3146

chr12: 817466

T/T

Fp(1/0)

T

TAT

aatctaaaaaatccaagtatg

cataatgattgtatatccttt

PF13_0184

chr13: 1376386

T/C

Fn(1/9)

T

T

tattcttgaattttcgctac

tatattttatggatcatctc

MAL13.4760

chr13: 2159993

C/T

Fn(0/2)

C

C

cacaaaagtatacgtctat

ttaacagtttaggacacata

MAL13.670

chr13: 304167

C/A

Fn(0/1)

A

A

attaaataattcttcttccag

catgtcttgtatttcgtttt

MAL13P1.67

chr13: 557320

A/T

Fn(0/3)

A

A

gttcttctaacacaaataaa

tctacaggtaatatgttatc

PF13_0088

chr13: 650502

T/C

Fn(0/4)

G

G

cggcatgctcctgaagtaaa

ttatgttagagatgggtata

PF13_0125

chr13: 912350

T/G

Fn(2/3)

A

G

catagtactatcacctgaa

ctatggttataaccaagaaat

MAL13P1.127

chr13: 958583

A/A

Fp(2/1)

T

C

gatgaatttgttgtaacgttt

acgttaataacaatcatgtga

MAL14.5217

chr14: 2364467

A/A

Fp(3/0)

A

A

ggtatatcctttctacatat

aattcttttcatagggagtt

PF14_0565

chr14: 2428920

A/T

Fn(16/23)

T

A

atcgtcaataccttcctcg

taaacaaaatatgagcactg

  1. Gene ID, gene ID or SNP ID in PlasmoDB; Chr position, chromosomal position of the polymorphic site; Mism Alle, mismatched alleles of our array calls and known NIAID SNP between 3D7 and 7G8; SFPn, calls not matching known SNP, either false positive (Fp) or false negative (Fn). The numbers in the parentheses are numbers of probes calling for SFP or no SFP. For example, Fp(3/0) indicates three probes called for a SFP and no probe called for no SFP, but there was no known SNP in the databases; and Fn(0/3) indicates three probes called for no SFP, but a known SNP existed (false negative); 3D7, alleles obtained from sequencing 3D7 DNA; and 7G8, alleles obtained from sequencing 7G8 DNA sequences. The gene ID in italic indicates SNP not confirmed by sequencing (true wrong calls) using 1.5 cutoff ratio and 3–23 positions in a probe; and those in bold had additional polymorphisms supporting the array calls. TAT in MAL12.3146 is a trinucleotide missing in 7G8. Forward and reverse are primers used in amplification and sequencing of the PCR products.
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BMC Genomics

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