TB-Profiler result

Run: ERR551512
Summary

Run ID: ERR551512

Sample name:

Date: 02-08-2023 08:29:20

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764363 p.Gly332Arg missense_variant 1.0 rifampicin
rrs 1472358 n.513C>T non_coding_transcript_exon_variant 1.0 streptomycin
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
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7782 p.Gln161* stop_gained 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491300 p.Tyr173Cys missense_variant 0.11
mshA 576751 p.Lys468Asn missense_variant 0.33
rpoB 760934 c.1128C>A synonymous_variant 0.11
rpoC 764878 c.1509C>A synonymous_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766422 p.Gly1018Asp missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777175 c.1304_1305dupAG frameshift_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673947 p.Glu170Lys missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154675 c.1437G>A synonymous_variant 0.12
katG 2154700 p.Gln471Arg missense_variant 1.0
katG 2154813 p.Lys433Asn missense_variant 0.11
katG 2154874 p.Tyr413Cys missense_variant 0.12
PPE35 2168046 p.Leu856Ser missense_variant 0.11
PPE35 2168236 p.Ala793Pro missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519093 p.Arg327Ser missense_variant 0.11
ahpC 2726338 p.Val49Gly missense_variant 0.17
ahpC 2726341 p.Val50Gly missense_variant 0.45
ahpC 2726350 p.Trp53Leu missense_variant 0.38
thyX 3067952 c.-7G>T upstream_gene_variant 0.11
thyX 3067954 c.-9G>C upstream_gene_variant 0.1
thyX 3067955 c.-10G>C upstream_gene_variant 0.1
thyX 3067957 c.-12A>C upstream_gene_variant 0.1
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612407 p.His237Arg missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 0.96
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267088 c.1749C>A synonymous_variant 0.11
ethR 4328102 c.555_560delGTCATT disruptive_inframe_deletion 0.11
ethR 4328111 p.Ala188Gly missense_variant 0.11
ethR 4328113 c.565_566insAATGAC stop_gained&disruptive_inframe_insertion 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0