TB-Profiler result

Run: SRR3732578
Summary

Run ID: SRR3732578

Sample name:

Date: 04-04-2023 05:36:03

Number of reads: 1885995

Percentage reads mapped: 99.53

Strain: lineage4.3.3

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 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
inhA 1674263 p.Ile21Thr missense_variant 1.0 isoniazid, ethionamide
katG 2155750 p.Gly121Val missense_variant 0.17 isoniazid
pncA 2289090 p.His51Arg missense_variant 1.0 pyrazinamide
embB 4248002 p.Gln497Lys 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 6865 c.-437G>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7469 c.168C>T synonymous_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575205 c.-143C>A upstream_gene_variant 0.12
rpoC 764335 c.966G>T synonymous_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765113 p.Val582Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777559 p.His308Asn missense_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407059 p.Trp94Cys missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473688 n.31C>T non_coding_transcript_exon_variant 0.11
rrl 1476292 n.2635G>A non_coding_transcript_exon_variant 0.33
rpsA 1834683 p.Ala381Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170480 p.Phe45Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746192 c.1407C>T synonymous_variant 0.14
folC 2746207 c.1392C>T synonymous_variant 0.17
folC 2746561 c.1038C>A synonymous_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074498 c.-27C>A upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475298 p.Arg431Leu missense_variant 0.13
fbiA 3640399 c.-144G>T upstream_gene_variant 0.13
rpoA 3878691 c.-184G>T upstream_gene_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040245 p.Gly154Cys missense_variant 0.14
embC 4241663 p.Gly601Trp missense_variant 0.12
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244288 c.1056C>A synonymous_variant 0.13
embA 4245698 p.Asn822Lys missense_variant 0.12
embB 4249233 p.Pro907His missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407768 p.Leu145Phe missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0