TB-Profiler result

Run: ERR6358868
Summary

Run ID: ERR6358868

Sample name:

Date: 02-04-2023 02:19:42

Number of reads: 5882432

Percentage reads mapped: 99.6

Strain: lineage4.6.1.1

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 1.0
lineage4.6.1.1 Euro-American T2-Uganda RD724 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
rpsL 781822 p.Lys88Thr missense_variant 0.11 streptomycin
katG 2155843 p.Trp90* stop_gained 0.2 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 0.11 pyrazinamide
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
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 0.99
gyrA 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.25
rpoC 767123 p.Val1252Leu missense_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
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154681 p.Trp477Tyr missense_variant 1.0
katG 2156100 c.12A>G synonymous_variant 0.13
Rv1979c 2222522 p.Lys215Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747481 p.Glu40Lys missense_variant 1.0
Rv2752c 3065587 p.Asp202Ala missense_variant 0.99
thyA 3074495 c.-24C>T upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4243201 c.-31delC upstream_gene_variant 1.0
embA 4245184 p.Leu651Arg missense_variant 0.99
embB 4246584 p.Arg24Pro missense_variant 0.24
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338378 c.141_143delCGA disruptive_inframe_deletion 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408009 p.Val65Gly missense_variant 1.0