TB-Profiler result

Run: ERR4827467
Summary

Run ID: ERR4827467

Sample name:

Date: 01-04-2023 18:04:26

Number of reads: 794283

Percentage reads mapped: 98.94

Strain: lineage4.5

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
lineage4.5 Euro-American H;T RD122 0.99
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.Ser315Ile missense_variant 1.0 isoniazid
embB 4247574 p.Asp354Ala missense_variant 0.96 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 7892 c.591G>A synonymous_variant 0.95
gyrA 8500 p.Ala400Gly missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoC 762983 c.-387C>T upstream_gene_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168225 c.2388C>A synonymous_variant 0.22
PPE35 2169049 p.Ile522Phe missense_variant 0.29
PPE35 2169082 p.Leu511Val missense_variant 0.25
PPE35 2170048 p.Leu189Val missense_variant 0.59
PPE35 2170053 p.Thr187Ser missense_variant 0.61
PPE35 2170454 c.159C>G synonymous_variant 0.12
PPE35 2170457 c.156G>C synonymous_variant 0.12
PPE35 2170521 p.Trp31* stop_gained 0.94
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223189 c.-25T>A upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289731 c.-490A>T upstream_gene_variant 0.12
pncA 2289737 c.-496A>G upstream_gene_variant 0.12
pncA 2289740 c.-499T>C upstream_gene_variant 0.12
pncA 2289903 c.-662C>T upstream_gene_variant 0.13
ahpC 2726285 c.93C>T synonymous_variant 0.12
folC 2746245 p.Ala452Thr missense_variant 0.13
folC 2746572 p.Arg343Cys missense_variant 0.22
folC 2746616 p.Ala328Asp missense_variant 0.18
thyX 3068028 c.-83G>T upstream_gene_variant 0.13
thyX 3068127 c.-182G>C upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612666 p.Val151Met missense_variant 1.0
Rv3236c 3612719 p.Ile133Thr missense_variant 0.17
fbiB 3642470 c.936G>A synonymous_variant 0.12
clpC1 4038318 p.Pro796Leu missense_variant 1.0
clpC1 4038483 p.Gln741Arg missense_variant 0.14
clpC1 4039425 p.Lys427Met missense_variant 0.11
embC 4240291 c.429G>A synonymous_variant 0.14
embC 4240608 p.His249Arg missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245708 c.2477delC frameshift_variant 0.2
embB 4245845 c.-669T>A upstream_gene_variant 0.2
embB 4246567 c.54_55insT frameshift_variant 0.18
embB 4249188 p.Tyr892Cys missense_variant 0.13
aftB 4268021 c.816G>T synonymous_variant 0.2
aftB 4268519 p.Tyr106* stop_gained 0.2
ubiA 4269879 c.-46C>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407727 p.Met159Pro missense_variant 1.0
gid 4407818 p.Gly129Cys missense_variant 1.0