TB-Profiler result

Run: ERR351926
Summary

Run ID: ERR351926

Sample name:

Date: 01-04-2023 02:36:10

Number of reads: 3576399

Percentage reads mapped: 99.56

Strain: lineage4.4;lineage3

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
lineage3 East-African-Indian CAS RD750 0.85
lineage4 Euro-American LAM;T;S;X;H None 0.14
lineage4.4 Euro-American S;T None 0.14
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 0.87 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
gyrA 9596 c.2295G>T synonymous_variant 0.8
fgd1 491367 c.585G>A synonymous_variant 0.24
fgd1 491742 c.960T>C synonymous_variant 0.88
rpoB 759746 c.-61C>T upstream_gene_variant 0.85
rpoC 762434 c.-936T>G upstream_gene_variant 0.84
rpoC 763031 c.-339T>C upstream_gene_variant 0.74
rpoC 764181 p.Asp271Gly missense_variant 0.81
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.83
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.64
rrl 1475357 n.1700C>T non_coding_transcript_exon_variant 0.79
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.82
katG 2155351 p.Arg254Leu missense_variant 0.84
PPE35 2167926 p.Leu896Ser missense_variant 0.83
PPE35 2170769 c.-157C>T upstream_gene_variant 0.85
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.86
pncA 2289365 c.-125delC upstream_gene_variant 0.86
eis 2714523 p.His270Gln missense_variant 0.16
eis 2714879 p.Asp152Asn missense_variant 0.86
ahpC 2726105 c.-88G>A upstream_gene_variant 0.88
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087118 p.Ser100Leu missense_variant 0.21
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 0.9
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247548 c.1035C>T synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.86