TB-Profiler result

Run: SRR12708386
Summary

Run ID: SRR12708386

Sample name:

Date: 02-08-2023 14:49:02

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage4.4.1.1.1

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
lineage4.4.1.1 Euro-American S;Orphans None 1.0
lineage4.4.1.1.1 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 761139 p.His445Tyr missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Asp 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 8095 p.Gly265Asp missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9380 p.Met693Ile missense_variant 0.12
mshA 576288 p.Arg314Gln missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776723 p.Tyr586* stop_gained 1.0
mmpL5 777423 p.Leu353Pro missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407059 p.Trp94Cys missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833959 p.Leu140Ile missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168995 p.Pro540Ala missense_variant 0.14
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064569 c.1623G>T synonymous_variant 0.15
Rv2752c 3064584 c.1608G>C synonymous_variant 0.14
thyX 3067644 p.Tyr101Phe missense_variant 0.2
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
fprA 3474227 p.Pro74His missense_variant 0.14
fprA 3474664 p.Gly220Trp missense_variant 0.13
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embC 4240174 c.312G>A synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0