TB-Profiler result

Run: ERR4818292
Summary

Run ID: ERR4818292

Sample name:

Date: 01-04-2023 15:28:38

Number of reads: 928076

Percentage reads mapped: 99.6

Strain: lineage4.6.2.2

Drug-resistance: HR-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
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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
katG 2155087 c.1024delG frameshift_variant 0.12 isoniazid
katG 2155168 p.Ser315Thr missense_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 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759887 c.81C>G synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778160 c.-830C>A upstream_gene_variant 0.13
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302782 c.-148delT upstream_gene_variant 0.12
Rv1258c 1406834 c.507C>G synonymous_variant 0.11
embR 1416576 p.Gln258* stop_gained 0.17
embR 1417011 p.Gly113Arg missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833416 c.-126T>C upstream_gene_variant 0.14
rpsA 1834811 p.Arg424Trp missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154548 p.Glu522Gln missense_variant 0.12
PPE35 2167719 p.Ser965Thr missense_variant 0.1
PPE35 2168961 p.Gly551Asp missense_variant 0.2
PPE35 2169690 p.Gly308Val missense_variant 0.18
PPE35 2170014 p.Gly200Ala missense_variant 0.12
PPE35 2170495 p.Ser40Pro missense_variant 0.13
PPE35 2170535 c.78G>A synonymous_variant 0.14
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2221752 c.1413T>C synonymous_variant 0.11
Rv1979c 2221859 p.Cys436Ser missense_variant 0.11
Rv1979c 2221928 p.Thr413Ala missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518617 p.Val168Ala missense_variant 0.17
kasA 2518915 c.801T>C synonymous_variant 0.12
kasA 2519016 p.Ser301Leu missense_variant 0.18
eis 2714353 p.Gly327Asp missense_variant 0.11
eis 2714735 p.Leu200Met missense_variant 0.11
pepQ 2859819 c.600G>A synonymous_variant 0.11
pepQ 2860335 p.Ile28Met missense_variant 0.12
Rv2752c 3065001 c.1191C>T synonymous_variant 0.12
Rv2752c 3066262 c.-71C>T upstream_gene_variant 0.17
thyX 3067517 p.Tyr143* stop_gained 0.14
Rv3083 3448567 p.His22Asp missense_variant 1.0
Rv3083 3449359 p.Phe286Leu missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475241 p.Ala412Gly missense_variant 0.11
Rv3236c 3612457 p.Leu220Phe missense_variant 0.18
Rv3236c 3612618 p.Pro167Ser missense_variant 0.15
fbiA 3641438 p.Asp299Gly missense_variant 0.11
ddn 3987042 c.199C>T synonymous_variant 0.14
clpC1 4038534 p.Arg724His missense_variant 0.12
clpC1 4039367 p.Lys446Asn missense_variant 0.12
clpC1 4039491 p.Glu405Val missense_variant 0.22
clpC1 4040646 p.Ala20Val missense_variant 0.12
embC 4239835 c.-28C>T upstream_gene_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245939 p.Gly903Ser missense_variant 0.11
embB 4246554 p.Arg14Gln missense_variant 1.0
embB 4247634 p.Gly374Glu missense_variant 1.0
embB 4249534 c.3022delG frameshift_variant 0.11
embB 4249743 p.Gln1077Arg missense_variant 0.12
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4268241 p.Met199Thr missense_variant 0.18
aftB 4268796 p.Ala14Val missense_variant 0.12
ethA 4326109 p.Trp455Cys missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4327479 c.-6G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
ethA 4328049 c.-576C>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407993 p.Ser70Arg missense_variant 1.0
gid 4408259 c.-57G>T upstream_gene_variant 0.12