TB-Profiler result

Run: ERR2513626
Summary

Run ID: ERR2513626

Sample name:

Date: 31-03-2023 19:48:14

Number of reads: 794546

Percentage reads mapped: 99.83

Strain: lineage4.3.4.2

Drug-resistance: Other

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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
ethA 4326604 c.869dupA frameshift_variant 0.1 ethionamide, ethionamide
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 6817 c.-485G>A upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576207 p.Ala287Asp missense_variant 0.12
ccsA 620362 p.Ala158Thr missense_variant 0.11
rpoC 762561 c.-809C>A upstream_gene_variant 0.12
rpoB 763110 p.Lys1102Glu missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777157 c.1324C>A synonymous_variant 0.13
mmpL5 777164 c.1317C>T synonymous_variant 0.13
mmpR5 779230 p.Glu81Lys missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 1.0
rrl 1476725 n.3068C>A non_coding_transcript_exon_variant 0.2
rpsA 1834558 c.1017C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102140 c.903C>A synonymous_variant 0.11
ndh 2102146 c.897G>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.2
PPE35 2170053 p.Thr187Ser missense_variant 0.22
PPE35 2170229 c.384A>G synonymous_variant 0.12
PPE35 2170232 c.381T>A synonymous_variant 0.12
PPE35 2170238 c.375T>G synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.1
eis 2715058 p.Arg92His missense_variant 0.15
ribD 2987171 p.Gln111His missense_variant 0.11
Rv2752c 3066102 p.Asn30Lys missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074430 c.42G>A synonymous_variant 0.1
thyA 3074645 c.-174T>G upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448378 c.-126C>T upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3641866 p.Ser111Tyr missense_variant 0.11
fbiB 3641936 c.402C>T synonymous_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040321 c.384C>A synonymous_variant 0.15
panD 4044121 p.Arg54Gln missense_variant 0.11
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embC 4240961 p.Leu367Met missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408442 c.-240G>A upstream_gene_variant 0.14