TB-Profiler result

Run: ERR4812829
Summary

Run ID: ERR4812829

Sample name:

Date: 01-04-2023 12:21:48

Number of reads: 2058055

Percentage reads mapped: 99.49

Strain: lineage4

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
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288775 c.456_466delCACCAGGGTGC frameshift_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala 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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761998 p.Leu731Pro missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766414 c.3045C>T synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777641 c.840C>T synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416505 c.843C>A synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473637 n.-21A>G upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746869 p.Val244Leu missense_variant 0.15
folC 2746989 p.Tyr204His missense_variant 0.12
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
fbiB 3641364 c.-171G>A upstream_gene_variant 0.29
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embB 4246569 p.Ala19Asp missense_variant 0.25
embB 4246930 p.Gln139His missense_variant 0.14
embB 4247147 c.637delC frameshift_variant 0.5
aftB 4268085 p.Ser251* stop_gained 0.13
ubiA 4269361 p.Leu158Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407973 p.Val77Gly missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408187 p.Pro6Ala missense_variant 0.4