TB-Profiler result

Run: ERR4819874

Summary

Run ID: ERR4819874

Sample name:

Date: 01-04-2023 16:21:15

Number of reads: 976461

Percentage reads mapped: 99.68

Strain: lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
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
gyrB 5076 c.-164_-163insT upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.25
rpoB 760548 p.Phe248Leu missense_variant 0.11
rpoC 764292 p.Ser308* stop_gained 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765621 p.Glu751Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102677 c.366C>T synonymous_variant 0.11
PPE35 2169796 p.Gly273Ser missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289251 c.-10T>A upstream_gene_variant 0.12
kasA 2518598 p.Ala162Pro missense_variant 0.11
eis 2715247 p.Gly29Asp missense_variant 0.11
folC 2747726 c.-128G>T upstream_gene_variant 0.14
Rv2752c 3065293 p.Val300Ala missense_variant 1.0
Rv2752c 3066083 c.109C>T synonymous_variant 0.12
Rv2752c 3066103 p.Asn30Ser missense_variant 0.1
thyX 3067329 p.Val206Ala missense_variant 0.17
thyX 3067807 p.Trp47Arg missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339397 p.Thr94Ala missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474744 p.Lys246Asn missense_variant 0.11
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embC 4240339 c.477G>A synonymous_variant 0.11
embC 4241455 p.Ile531Met missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326526 c.948C>A synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408060 p.His48Pro missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0