TB-Profiler result

Run: SRR18715065
Summary

Run ID: SRR18715065

Sample name:

Date: 03-04-2023 20:17:20

Number of reads: 1782249

Percentage reads mapped: 99.63

Strain: 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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.17
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.27
rpoB 760106 c.300G>A synonymous_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764714 p.Leu449Val missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777128 c.1353A>G synonymous_variant 0.12
mmpL5 777883 p.Gly200Arg missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474545 n.888G>A non_coding_transcript_exon_variant 0.17
rrl 1474666 n.1009T>C non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.15
PPE35 2169910 p.Asn235Tyr missense_variant 0.2
PPE35 2170065 p.Ala183Gly missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289045 p.Ser66* stop_gained 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.21
pepQ 2860159 p.Ala87Gly missense_variant 0.19
thyX 3067864 p.Asp28Tyr missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.95
whiB7 3568433 p.Arg83Gly missense_variant 0.22
rpoA 3878641 c.-134C>G upstream_gene_variant 0.75
embC 4240409 p.Pro183Ala missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246539 p.Lys9Arg missense_variant 0.18
embB 4247028 p.Leu172Arg missense_variant 0.29
embB 4247033 p.Ser174Arg missense_variant 0.21
ethA 4328415 c.-942A>G upstream_gene_variant 0.2
whiB6 4338200 p.Asp108His missense_variant 0.16
whiB6 4338513 c.9C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407721 p.Ala161Asp missense_variant 1.0