TB-Profiler result

Run: SRR23310988

Summary

Run ID: SRR23310988

Sample name:

Date: 14-03-2023 05:44:49

Number of reads: 2270078

Percentage reads mapped: 99.52

Strain: lineage4.2.1.1

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
lineage4.2 Euro-American H;T;LAM None 0.98
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.99
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 0.97
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
rpsL 781822 p.Lys88Arg missense_variant 0.96 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289159 p.Ala28Asp missense_variant 0.43 pyrazinamide
pncA 2289193 c.48_49insA frameshift_variant 0.54 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326419 c.1051delG frameshift_variant 0.49 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 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.19
mshA 576616 c.1269G>C synonymous_variant 0.33
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776802 p.Met560Thr missense_variant 0.99
mmpL5 777451 p.Val344Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303485 c.555C>T synonymous_variant 0.53
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.45
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.24
Rv2752c 3065958 c.234G>A synonymous_variant 0.99
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.6
fbiD 3339746 p.Ala210Gly missense_variant 0.6
fbiD 3339751 p.Ala212Pro missense_variant 0.21
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.2
rpoA 3878597 c.-90G>C upstream_gene_variant 0.22
rpoA 3878637 c.-130G>C upstream_gene_variant 0.75
rpoA 3878641 c.-134C>G upstream_gene_variant 0.67
ddn 3987092 p.Glu83Asp missense_variant 0.97
clpC1 4040786 c.-82G>A upstream_gene_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246529 p.Ser6Arg missense_variant 0.25
embB 4246584 p.Arg24Pro missense_variant 0.3
ethA 4326716 p.Cys253Phe missense_variant 0.42
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 0.99