TB-Profiler result

Run: ERR4815990
Summary

Run ID: ERR4815990

Sample name:

Date: 01-04-2023 14:10:45

Number of reads: 1026516

Percentage reads mapped: 99.82

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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575296 c.-52C>A upstream_gene_variant 0.11
mshA 576651 p.Asp435Gly missense_variant 0.1
rpoB 762041 c.2235C>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777256 p.Pro409Ser missense_variant 0.12
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801257 p.Ser150Tyr missense_variant 0.11
fbiC 1303030 c.100C>A synonymous_variant 0.11
fbiC 1303349 p.Cys140Phe missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 1.0
rrs 1472687 n.842A>G non_coding_transcript_exon_variant 0.18
rrl 1475188 n.1531C>G non_coding_transcript_exon_variant 0.18
rrl 1475204 n.1547C>A non_coding_transcript_exon_variant 0.17
rrl 1476097 n.2440C>A non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918434 c.495C>T synonymous_variant 0.12
katG 2154620 p.Arg498Cys missense_variant 0.15
katG 2155389 c.723C>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223149 p.Thr6Ala missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289166 p.Ala26Thr missense_variant 0.11
pncA 2289168 p.Ala25Asp missense_variant 0.12
kasA 2518775 p.Asp221Asn missense_variant 0.11
folC 2746716 p.Gly295Cys missense_variant 0.18
thyX 3067474 p.Pro158Ala missense_variant 1.0
ald 3087178 p.Val120Ala missense_variant 0.11
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474373 p.Ile123Phe missense_variant 0.11
fprA 3474857 p.Val284Ala missense_variant 0.1
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612910 p.Leu69Phe missense_variant 1.0
Rv3236c 3613018 c.99T>C synonymous_variant 0.13
embC 4242380 p.Pro840Ser missense_variant 0.11
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243436 c.204C>T synonymous_variant 0.11
embA 4244607 c.1375C>T synonymous_variant 0.11
embB 4246181 c.-333C>T upstream_gene_variant 0.13
embB 4247332 p.Trp273* stop_gained 0.12
embB 4249396 c.2883C>T synonymous_variant 0.15
embB 4249532 p.Ala1007Thr missense_variant 0.18
embB 4249698 p.Gly1062Asp missense_variant 0.29
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4268103 p.Ala245Val missense_variant 0.14
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0