TB-Profiler result

Run: SRR023452
Summary

Run ID: SRR023452

Sample name:

Date: 02-04-2023 14:12:05

Number of reads: 5286126

Percentage reads mapped: 97.15

Strain: lineage4.1.2.1

Drug-resistance: RR-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 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
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 491414 p.Val211Gly missense_variant 0.37
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 0.94
rpoB 760115 c.309C>T synonymous_variant 0.96
rpoC 765150 p.Gly594Glu missense_variant 0.96
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777502 p.Thr327Pro missense_variant 0.23
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304071 p.Thr381Pro missense_variant 0.44
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673449 p.Thr4Pro missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155375 p.Val246Gly missense_variant 0.2
katG 2155726 p.Phe129Ser missense_variant 1.0
PPE35 2170357 p.Ala86Ser missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518144 c.30T>G synonymous_variant 0.24
kasA 2518163 p.Thr17Pro missense_variant 0.15
eis 2715098 p.Thr79Pro missense_variant 0.18
pepQ 2860126 p.Glu98Gly missense_variant 0.15
thyA 3074654 c.-183T>G upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612422 p.Val232Gly missense_variant 0.18
rpoA 3877949 p.Thr187Ala missense_variant 1.0
rpoA 3878647 c.-140delG upstream_gene_variant 0.12
ddn 3986929 p.Tyr29Ser missense_variant 0.14
embC 4240619 p.Thr253Pro missense_variant 0.14
embC 4241429 p.Phe523Val missense_variant 0.36
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4247822 p.Thr437Pro missense_variant 0.22
embB 4247868 p.Val452Ala missense_variant 0.33
embB 4248614 p.Ala701Thr missense_variant 1.0
ubiA 4269317 p.Ser173Ala missense_variant 1.0