TB-Profiler result

Run: ERR11049114
Summary

Run ID: ERR11049114

Sample name:

Date: 31-03-2023 11:04:01

Number of reads: 356970

Percentage reads mapped: 99.51

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 2155697 p.Ala139Pro missense_variant 0.25 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 9087 p.Val596Met missense_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.18
fgd1 490992 c.210G>A synonymous_variant 0.15
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620842 p.His318Tyr missense_variant 0.2
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761527 p.Asp574Gly missense_variant 0.25
rpoC 764586 p.Leu406Arg missense_variant 0.5
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778498 c.-18C>T upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406970 p.Arg124His missense_variant 0.22
embR 1417400 c.-53C>A upstream_gene_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473935 n.278C>T non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918347 c.408A>C synonymous_variant 0.25
tlyA 1918622 p.Ser228Thr missense_variant 0.33
katG 2154042 c.2070C>T synonymous_variant 0.2
katG 2155544 p.Gln190Glu missense_variant 0.18
katG 2156360 c.-249T>A upstream_gene_variant 0.5
Rv1979c 2221864 p.Tyr434Cys missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2747623 c.-25T>C upstream_gene_variant 0.29
pepQ 2860183 p.Val79Gly missense_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449936 p.Ile478Asn missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641402 p.Cys287Tyr missense_variant 0.33
fbiB 3641505 c.-30C>T upstream_gene_variant 0.2
clpC1 4040691 p.Phe5Tyr missense_variant 0.18
embC 4240380 p.Gln173Arg missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245925 p.Val898Gly missense_variant 0.22
embB 4249219 c.2706C>T synonymous_variant 0.2
ethA 4328025 c.-552T>A upstream_gene_variant 0.22
ethA 4328435 c.-962C>T upstream_gene_variant 1.0
whiB6 4338200 p.Asp108His missense_variant 0.29
whiB6 4338396 c.126G>C synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408142 p.Arg21Trp missense_variant 0.25