TB-Profiler result

Run: SRR9224914
Summary

Run ID: SRR9224914

Sample name:

Date: 04-04-2023 22:06:39

Number of reads: 736757

Percentage reads mapped: 87.19

Strain: lineage4.3.4.1

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 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 0.99
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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
embB 4249583 p.Asp1024Asn 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
fgd1 491489 p.Asp236Ala missense_variant 0.27
rpoB 761496 p.Tyr564His missense_variant 0.19
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461096 p.Ala18Thr missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674205 p.Thr2Pro missense_variant 0.15
rpsA 1833918 p.Val126Gly missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167793 p.Ile940Met missense_variant 0.12
PPE35 2169906 p.Asn236Thr missense_variant 0.14
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0
Rv1979c 2223245 c.-81T>G upstream_gene_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726587 p.Asp132Ala missense_variant 0.25
folC 2747562 p.Ser13Pro missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039991 c.714G>A synonymous_variant 1.0
clpC1 4040605 p.Leu34Ile missense_variant 0.32
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407790 p.Ala138Val missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0