TB-Profiler result

Run: ERR4830851
Summary

Run ID: ERR4830851

Sample name:

Date: 01-04-2023 20:30:06

Number of reads: 2535554

Percentage reads mapped: 96.05

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 0.99
lineage4.4.1.1 Euro-American S;Orphans None 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 761277 p.Ile491Phe missense_variant 0.98 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289091 p.His51Asp missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 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 9138 p.Gln613Glu missense_variant 0.95
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.24
rpoC 766467 p.Glu1033Ala missense_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304891 p.Ile654Thr missense_variant 0.12
fbiC 1304893 p.Gly655Ser missense_variant 0.12
fbiC 1304907 c.1977C>G synonymous_variant 0.12
fbiC 1304910 c.1980G>C synonymous_variant 0.12
fbiC 1304916 c.1986T>C synonymous_variant 0.12
fbiC 1304928 c.1998T>C synonymous_variant 0.14
fbiC 1304937 c.2007G>C synonymous_variant 0.15
fbiC 1304958 c.2028T>G synonymous_variant 0.12
fbiC 1304995 p.Leu689Met missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.11
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.11
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.11
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.12
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518496 c.382C>T synonymous_variant 1.0
Rv2752c 3065023 p.Pro390Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.25
Rv3083 3448522 p.Val7Phe missense_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 0.99
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.52
whiB6 4338595 c.-75delG upstream_gene_variant 1.0