TB-Profiler result

Run: SRR2101775
Summary

Run ID: SRR2101775

Sample name:

Date: 03-04-2023 23:54:30

Number of reads: 563588

Percentage reads mapped: 99.66

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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 761140 p.His445Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575764 c.417C>A synonymous_variant 0.18
ccsA 620519 p.Gly210Asp missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673463 c.-739G>T upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101981 c.1062C>G synonymous_variant 0.25
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168205 p.Pro803Gln missense_variant 0.17
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859920 p.Arg167* stop_gained 0.2
Rv2752c 3065242 p.Arg317Pro missense_variant 1.0
thyX 3067919 c.27G>T synonymous_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embC 4240763 p.Ala301Ser missense_variant 0.1
embC 4242459 p.Ser866* stop_gained 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245639 p.Asn803His missense_variant 0.22
embB 4248896 p.Glu795* stop_gained 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0