TB-Profiler result

Run: ERR3287830
Summary

Run ID: ERR3287830

Sample name:

Date: 01-04-2023 01:41:31

Number of reads: 2721002

Percentage reads mapped: 99.61

Strain: lineage4.1.2.1

Drug-resistance: Pre-XDR-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
gyrB 6620 p.Asp461Asn missense_variant 0.78 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrB 6750 p.Ala504Val missense_variant 0.62 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.22 kanamycin, capreomycin, aminoglycosides, amikacin
tlyA 1918135 c.198_199delAG frameshift_variant 0.14 capreomycin
tlyA 1918331 c.395_398dupAGCG frameshift_variant 0.12 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 0.19 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4408137 p.Tyr22* stop_gained 1.0 streptomycin
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
gyrB 6735 p.Asn499Ser missense_variant 0.11
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 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918489 p.Gln184Lys missense_variant 0.12
PPE35 2169547 p.His356Tyr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288859 p.Val128Asp missense_variant 0.77
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612846 p.Pro91Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ethA 4326356 p.Met373Thr missense_variant 0.16
ethA 4327088 p.Leu129Pro missense_variant 0.83
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
PPE35 2165655 c.1065_*1993del frameshift_variant&stop_lost&splice_region_variant 1.0