TB-Profiler result

Run: ERR4812779
Summary

Run ID: ERR4812779

Sample name:

Date: 01-04-2023 12:19:49

Number of reads: 402975

Percentage reads mapped: 98.71

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 0.93
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.93
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 761095 p.Leu430Pro missense_variant 0.8 rifampicin
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
gyrA 9620 c.2319G>A synonymous_variant 0.83
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 0.89
mshA 575830 c.483C>A synonymous_variant 0.13
rpoB 760115 c.309C>T synonymous_variant 0.93
rpoB 761889 p.Val695Leu missense_variant 0.38
rpoC 763421 p.Glu18Lys missense_variant 0.22
rpoC 764817 p.Val483Gly missense_variant 0.25
rpoC 765150 p.Gly594Glu missense_variant 0.78
rpoC 765981 p.Gly871Val missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776873 p.Met536Ile missense_variant 0.2
mmpL5 777875 c.605delG frameshift_variant 0.67
mmpL5 778738 c.-258G>T upstream_gene_variant 0.18
mmpR5 779042 p.Glu18Val missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303594 p.Leu222Met missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472783 n.938G>T non_coding_transcript_exon_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156173 c.-62C>A upstream_gene_variant 0.2
PPE35 2169195 p.Pro473His missense_variant 0.33
PPE35 2170278 p.Ala112Val missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.93
kasA 2518375 c.261C>A synonymous_variant 0.12
ahpC 2726714 p.Cys174Trp missense_variant 0.2
folC 2746187 p.Ser471* stop_gained 0.22
folC 2747405 p.Pro65Gln missense_variant 0.18
ribD 2987321 p.Glu161Asp missense_variant 0.29
ribD 2987348 c.510G>T synonymous_variant 0.33
thyA 3074495 c.-24C>T upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 0.91
ald 3087292 p.Val158Ala missense_variant 0.22
Rv3083 3448924 p.Gly141Ser missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.89
rpoA 3878619 c.-112A>C upstream_gene_variant 0.33
embC 4240180 c.318G>A synonymous_variant 0.33
embC 4240649 p.Leu263Met missense_variant 0.29
embC 4240914 p.Met351Thr missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243126 c.-107G>A upstream_gene_variant 0.17
ethR 4326562 c.-987G>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0