TB-Profiler result

Run: ERR11080995
Summary

Run ID: ERR11080995

Sample name:

Date: 08-04-2023 01:35:02

Number of reads: 2126671

Percentage reads mapped: 99.64

Strain: lineage4.3.3;lineage4.2.1.1

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 0.63
lineage4.2 Euro-American H;T;LAM None 0.41
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.36
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.6
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 0.38
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 761140 p.His445Leu missense_variant 0.46 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.32 streptomycin
fabG1 1673423 c.-17G>T upstream_gene_variant 0.46 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.41 isoniazid
pncA 2289111 p.Val44Gly missense_variant 0.45 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.37 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.39 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 7058 p.Ile607Val missense_variant 0.65
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.45
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620511 c.621C>T synonymous_variant 0.44
rpoC 764995 c.1626C>G synonymous_variant 0.64
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 0.34
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.62
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.6
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103023 p.Pro7Leu missense_variant 0.37
katG 2156196 c.-85C>T upstream_gene_variant 0.52
PPE35 2169879 p.Phe245Cys missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.66
folC 2746340 p.Ala420Val missense_variant 0.65
thyA 3073868 p.Thr202Ala missense_variant 0.58
ald 3086742 c.-78A>C upstream_gene_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878630 c.-123G>C upstream_gene_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 0.48
clpC1 4038968 c.1737G>A synonymous_variant 0.53
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268566 p.Ser91Ala missense_variant 0.55
ethA 4327377 p.Ala33Pro missense_variant 0.37
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407598 p.Val202Glu missense_variant 0.4
gid 4408156 p.Leu16Arg missense_variant 0.57
gid 4408213 c.-11C>T upstream_gene_variant 0.41