TB-Profiler result

Run: ERR4818585
Summary

Run ID: ERR4818585

Sample name:

Date: 01-04-2023 15:38:31

Number of reads: 1170958

Percentage reads mapped: 98.75

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
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
rrs 1472093 n.248T>G non_coding_transcript_exon_variant 0.25
rrl 1475502 n.1845A>C non_coding_transcript_exon_variant 0.4
rrl 1475737 n.2080G>A non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155873 p.Ile80Thr missense_variant 0.14
PPE35 2170173 c.437_439dupTGG conservative_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518659 p.Trp182Leu missense_variant 0.14
folC 2747633 c.-35A>G upstream_gene_variant 0.11
thyX 3067437 p.Ala170Val missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339423 c.306G>T synonymous_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474725 p.Ala240Glu missense_variant 0.12
Rv3236c 3612691 c.426G>T synonymous_variant 0.17
fbiB 3642132 p.Ala200Thr missense_variant 0.18
embC 4240059 p.Thr66Lys missense_variant 0.13
embC 4241745 p.Phe628Ser missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242806 p.Phe982Ile missense_variant 1.0
embA 4243730 p.Lys166Asn missense_variant 1.0
embA 4245447 p.Val739Leu missense_variant 0.2
aftB 4267943 c.894C>T synonymous_variant 0.15
aftB 4268582 c.255C>A synonymous_variant 0.17
ethA 4326996 p.Pro160Thr missense_variant 1.0
ethR 4327967 p.Thr140Met missense_variant 0.13
whiB6 4338306 c.216G>T synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0