Table 3 Genes with k-mers significantly associated with clustered strains harboring katG-S315T mutation (cluster[+]/S315T[+]) in both Hanoi and KwaZulu-Natal study cohorts, further investigated by using the DBGWAS platform and variant/deletion-based search.

From: Whole genome sequencing, analyses of drug resistance-conferring mutations, and correlation with transmission of Mycobacterium tuberculosis carrying katG-S315T in Hanoi, Vietnam

Gene name

Sample panel

K-mer-based GWAS

Strongest P value

DBGWAS*

Strongest P value

Variant-based GWAS/deletion-based GWAS/BLAST search

Strongest P value

Conclusion on variant(s) corresponding to significant k-mer(s)

PPE18/19

Hanoi

36 k-mers, SNV at 1339644 and 1339649

1.840E-09

1 unitig, SNVs at 1339644 and 1339649

5.56188E-07

SNVs at 1339644 (E99A) and 1339649 (A101T) found by variant-based GWAS

1.941E-09

Significant SNVs E99A and A101T

PPE18/19

KwaZulu-Natal

5 k-mers, SNV at 1340231

2.998E-08

1 unitig**, SNV at 1532777

4.8561E-10

SNV at 1532777 (Q286R) detected by BLAST search. By variant-based GWAS, SNV was not called properly

NA

SNV Q286R

gid

Hanoi

33 k-mers, SNV at 4407686

5.213E-08

3 unitgs, SNV at 4407686

3.676E-05

SNV at 4407686 (E173*) fount by variant-based GWAS

2.991E-06

Significant SNV E173*

gid

KwaZulu-Natal

101 k-mers

7.802E-07

7 unitigs, no SNV

7.943E-09

Large deletions (from 120 bp to 675 bp)

2.178E-04

Large deletions

emrB

Hanoi

31 k-mers, SNV at 876918

8.579E-08

2 unitigs, SNV at 876918

1.704E-05

SNV at 876918 (F508S) found by variant-based GWAS

1.507E-08

Significant SNV F508S

emrB

KwaZulu-Natal

31 k-mers, SNV at 877058

7.802E-07

2 unitigs**, SNV at 877058

7.943E-09

SNV at 877058 (I461I) found by variant-based GWAS

1.077E-06

Significant SNV I461I

Rv1588c

Hanoi

4 k-mers without SNV (neg.***)

8.579E-08

2 unitigs**, no SNV

1.704E-05

SNV at 1789735 (P34P) found by variant-based GWAS and BLAST search

1.511E-08

Significant SNV P34P

Rv1588c

KwaZulu-Natal

12 k-mers without SNV (neg.***)

2.453E-06

0 unitig

NA

No SNV inside the corresponding k-mers

NA

None

pncA

Hanoi

31 k-mers without SNV (neg.***)

4.437E-07

0 unitig (pncA not found)

NA

SNV at 2288820 (Q141P) found by variant-based GWAS

4.919E-07

Significant SNV Q141P

pncA

KwaZulu-Natal

29 k-mers, SNV at 2288785 and 2288788

4.802E-11

1 unitig, G insertion at 2288785

7.639E-12

SNV at 2288785 (T153fs) found by variant-based GWAS

6.569E-11

Significant SNV T153fs

  1. cluster[+]: clustered (pairwise SNV difference between two isolates is no more than five SNVs); S315T[+]: harboring katG-S315T mutation; Hanoi: Hanoi’s study cohort; KwaZulu-Natal: KwaZulu-Natal’s study cohort; GWAS: genome wide association study; SNV: single nucleotide variant.
  2. *Only significant unitigs and their SNVs are shown.
  3. **Found by sequence search.
  4. ***Showing negative association with Cluster[+]/S315T[+] by logistic regression analyses
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