TB-Profiler result

Run: ERR2510565

Summary

Run ID: ERR2510565

Sample name:

Date: 31-03-2023 18:48:56

Number of reads: 1121948

Percentage reads mapped: 99.46

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 761139 p.His445Tyr missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>G upstream_gene_variant 0.11 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2156040 c.70_71dupGG frameshift_variant 0.24 isoniazid, isoniazid
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491610 c.828A>G synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760988 c.1182C>G synonymous_variant 0.1
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765461 p.Asn698Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472986 n.1141C>T non_coding_transcript_exon_variant 1.0
rrs 1473285 n.1440A>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153903 p.Phe737Ile missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155055 p.Tyr353His missense_variant 0.32
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518609 p.Met165Ile missense_variant 0.1
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyA 3074495 c.-24C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448597 p.Ile32Phe missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877642 p.Phe289Ser missense_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4269099 c.-263G>T upstream_gene_variant 0.12
ubiA 4269161 p.Ser225Pro missense_variant 0.12
ubiA 4269307 p.Phe176Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407797 p.Ser136Pro missense_variant 1.0
pncA 2288842 c.280_399del conservative_inframe_deletion 1.0