Table 1 Non-canonical regions confirmed in the second validation GWAS and four canonical regions for comparison

From: GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions

Locus/site

Drug

AF

Scaled effect size

Scaled SE

P value raw

Drug

AF

OR

SE

P value raw

ubiA (Rv3806c)

EMB, INH, RIF, PZA, KAN

0.071

0.52

0.07

1E-13

EMB, INH, RIF, PZA

0.066

1.25

0.10

3.6E-03

Rv3805c - 4267647 T > C (D397G)

AMI

0.050

2.72

0.63

4E-06

AMI

0.283

1.11

0.03

4.7E-04

dinG†

RIF

0.069

1.86

0.47

2E-05

AMI, STR

0.293

1.10

0.03

8.8E-04

whiB6^

CAP, AMI, KAN

0.037

0.59

0.15

3E-05

CAP, AMI

0.069

1.16

0.06

2.7E-03

RNase J (Rv2752c)

INH, RIF

0.042

0.77

0.20

8E-05

KAN, AMI, RIF, INH

0.067

1.29

0.06

2.8E-08

sirA

ETA

0.070

0.78

0.21

1E-04

CAP, KAN, STR

0.015

1.27

0.09

8.0E-04

PPE35

PZA

0.112

0.54

0.14

1E-04

EMB

0.334

1.24

0.08

4.9E-04

Rv3434c*

KAN, AMI

0.048

1.14

0.33

1E-04

KAN, AMI

0.047

1.18

0.06

2.3E-03

espK-espL

RFB, RIF

0.053

1.21

0.34

2E-04

AMI, STR

0.283

1.11

0.03

4.7E-04

Rv2952**

EMB

0.067

0.64

0.17

2E-04

STR,AMI INH,CAP

0.203

1.29

0.08

2.6E-05

ccsA

KAN

0.052

1.64

0.47

3E-04

AMI, CAP

0.274

1.11

0.03

2.7E-04

thyX-hsdS.1

AMI

0.018

0.74

0.22

3E-04

STR

0.016

1.32

0.13

3.9E-03

kefB (Rv3236c)***

PZA

0.137

0.80

0.24

6E-04

RIF,INH, PZA,EMB STR

0.235

1.60

0.16

2.0E-06

inhA

INH

0.03

1.10

0.26

2E-05

 

–

   

Rv1482c-fabG1

INH

0.10

0.63

0.16

6E-05

 

–

   

pncA

PZA

0.24

1.40

0.07

4E-89

 

–

   

pncA-Rv2044c

PZA

0.01

0.81

0.20

7E-5

 

–

   
  1. All drugs to which they were found to be associated are listed. The first drug listed was the drug found to be most significantly associated and for which the GWAS results are listed in the subsequent columns. Left half of the table represents the test GWAS results (n = 1452) and the rightward half lists results of the validation (n = 792). Four known/canonical resistance loci are also listed along with their respective allele frequency, effect size, and P value for comparison. Full results detailed in Supplementary Data Files 2–3. Drug abbreviations detailed in Supplementary Table 2. AF: allele frequency. OR: odds ratio. SE standard error. Scaled effect size and SE are on the logMIC scale. *transmembrane protein, **integral membrane transport protein, ***probable methyl transferase and membrane protein, ^transcriptional regulator, †structure-specific helicase
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