TB-Profiler result

Run: ERR6358927
Summary

Run ID: ERR6358927

Sample name:

Date: 02-04-2023 02:24:39

Number of reads: 6307454

Percentage reads mapped: 99.58

Strain: lineage4.7;lineage4.6.1.2

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
lineage4.6 Euro-American T;LAM None 0.86
lineage4.7 Euro-American (mainly T) T1;T5 None 0.13
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.87
lineage4.6.1.2 Euro-American T2 RD724 0.86
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 0.88 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
gyrB 6798 p.Gly520Ala missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 0.85
gyrA 7585 p.Ser95Thr missense_variant 0.88
gyrA 9304 p.Gly668Asp missense_variant 0.84
mshA 575578 c.231G>C synonymous_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 0.91
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101786 c.1257G>A synonymous_variant 0.87
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065954 p.Thr80Ala missense_variant 0.88
Rv2752c 3066208 c.-17C>G upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.86
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 0.87
embB 4246584 p.Arg24Pro missense_variant 0.28
embB 4248175 c.1662G>T synonymous_variant 0.86
embB 4249732 c.3219C>G synonymous_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0