Global-scale GWAS associates a subset of SNPs with animal-adapted variants in M. tuberculosis complex

BMC Medical Genomics

Table 5 SNP typing improperly labeled MBO isolate by MTB-lineage markers

Lineage Marker	Lineage 2	Lineage 2	Lineage 2	Lineage 2	Lineage 2.2	Lineage 2.2	Lineage 2.2	Lineage 2.2.1	Lineage 2.2.1
Accession ID	G497491A	C811753T	A1834177C	T2543395C	C1849051T	G2505085A	C2775361T	C797736T	C3498198T
SRR16278270	✓	✓	✓	✓	✓	✓	✓	✓	✓

Isolate SRR16278270 was deposited in NCBI as an MBO isolate from cattle, but its genotype by GWAS did not align with other MBO isolates. This isolate was checked for MTB lineage-determining SNPs as reported by Coll et al. [24], and was found to contain all SNPs for MTB lineage 2.2.1 and none for MBO (Table 4), indicating a misclassification in the database. This was confirmed by SNP-IT [25]

ISSN: 1755-8794