TB-Profiler result

Run: ERR4831850
Summary

Run ID: ERR4831850

Sample name:

Date: 20-10-2023 13:04:14

Number of reads: 2631969

Percentage reads mapped: 97.08

Strain: lineage4.1.2

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
Rifampicin
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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 0.97
lineage4.1.2 Euro-American T;H None 0.98
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 490892 p.Val37Gly missense_variant 1.0
rpoC 763031 c.-339T>G upstream_gene_variant 0.1
rpoC 763040 c.-330C>G upstream_gene_variant 0.1
rpoC 765150 p.Gly594Glu missense_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417140 p.Ala70Ser missense_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 0.98
rrs 1472846 n.1001C>T non_coding_transcript_exon_variant 0.26
rrs 1472847 n.1002G>A non_coding_transcript_exon_variant 0.26
rrs 1472848 n.1003T>C non_coding_transcript_exon_variant 0.27
rrs 1472860 n.1015C>T non_coding_transcript_exon_variant 0.33
rrs 1472861 n.1016G>A non_coding_transcript_exon_variant 0.33
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.18
fabG1 1673249 c.-191C>T upstream_gene_variant 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169202 p.Ser471Ala missense_variant 0.92
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747022 p.Val193Ile missense_variant 0.93
Rv2752c 3065377 p.Val272Ala missense_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449642 p.Asn380Ser missense_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641164 p.Ile208Val missense_variant 0.95
ddn 3986755 c.-89G>C upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ethA 4327265 p.Thr70Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408048 p.Cys52Phe missense_variant 0.97