TB-Profiler result

Run: ERR7975670

Summary

Run ID: ERR7975670

Sample name:

Date: 02-04-2023 07:18:43

Number of reads: 1487252

Percentage reads mapped: 99.64

Strain: lineage4.3.3;lineage4.1.2.1

Drug-resistance: MDR-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 0.28
lineage4.1 Euro-American T;X;H None 0.73
lineage4.1.2 Euro-American T;H None 0.7
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.32
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.69
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
rpoB 761109 p.Asp435Tyr missense_variant 0.31 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.37 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.37 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.3 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491038 p.Ile86Val missense_variant 0.1
fgd1 491591 p.Lys270Met missense_variant 0.63
mshA 575679 p.Asn111Ser missense_variant 0.65
rpoB 759615 c.-192A>C upstream_gene_variant 0.2
rpoB 760115 c.309C>T synonymous_variant 0.64
rpoC 764995 c.1626C>G synonymous_variant 0.31
rpoC 765150 p.Gly594Glu missense_variant 0.72
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779237 c.251_252delCG frameshift_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.34
fbiC 1304962 p.Trp678Gly missense_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.16
PPE35 2170159 p.Ala152Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.8
kasA 2518919 p.Gly269Ser missense_variant 0.29
ahpC 2726341 p.Val50Gly missense_variant 0.21
folC 2746340 p.Ala420Val missense_variant 0.4
ribD 2986827 c.-12G>A upstream_gene_variant 0.47
thyA 3073868 p.Thr202Ala missense_variant 0.37
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.11
clpC1 4038968 c.1737G>A synonymous_variant 0.32
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.65
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.38