TB-Profiler result

Run: SRR6484867
Summary

Run ID: SRR6484867

Sample name:

Date: 04-04-2023 14:49:37

Number of reads: 1829121

Percentage reads mapped: 99.78

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 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4249512 p.Met1000Arg 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
gyrB 6573 p.Cys445Phe missense_variant 0.17
gyrA 7307 c.6A>T synonymous_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
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 576108 p.Ala254Gly 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471740 n.-106A>T upstream_gene_variant 0.67
rrs 1472928 n.1083A>T non_coding_transcript_exon_variant 0.2
fabG1 1673346 c.-94C>G upstream_gene_variant 0.13
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
fabG1 1673560 p.Lys41His missense_variant 0.12
rpsA 1834836 p.Met432Thr missense_variant 1.0
rpsA 1834916 p.Thr459Pro missense_variant 0.22
tlyA 1917811 c.-129T>C upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 1.0
PPE35 2168367 p.Leu749* stop_gained 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714185 p.Leu383His missense_variant 0.13
folC 2746340 p.Ala420Val missense_variant 0.9
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
fprA 3474935 p.Arg310Pro missense_variant 0.1
fbiB 3642150 p.Lys206* stop_gained 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.3
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246584 p.Arg24Pro missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407704 p.Ala167Pro missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0