TB-Profiler result

Run: ERR234187

Summary

Run ID: ERR234187

Sample name:

Date: 31-03-2023 18:02:32

Number of reads: 4302528

Percentage reads mapped: 99.57

Strain: lineage4.6.2.2

Drug-resistance: HR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.44
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.26
PPE35 2169866 c.747G>C synonymous_variant 0.17
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.92
Rv1979c 2222531 p.Glu212Lys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.32
Rv2752c 3064552 p.Arg547Pro missense_variant 0.31
Rv2752c 3065479 p.Phe238Cys missense_variant 0.29
fbiD 3339273 c.156T>G synonymous_variant 0.17
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.17
clpC1 4038857 c.1848C>A synonymous_variant 0.29
clpC1 4039932 p.Gly258Val missense_variant 0.35
embC 4239842 c.-21C>A upstream_gene_variant 0.12
embC 4239887 p.Arg9Cys missense_variant 1.0
embC 4241429 p.Phe523Val missense_variant 0.38
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.33
aftB 4267272 p.Lys522Arg missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.19
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0