TB-Profiler result

Run: ERR1035315
Summary

Run ID: ERR1035315

Sample name:

Date: 20-10-2023 21:38:43

Number of reads: 6245207

Percentage reads mapped: 98.43

Strain: lineage4.3.4.1

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
Rifampicin R rpoB p.Ser450Leu (0.99)
Isoniazid R fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (1.00)
Ethambutol R embA c.-12C>T (0.97), embB p.Met306Ile (0.99)
Pyrazinamide R pncA p.Asp63His (1.00)
Streptomycin R rpsL p.Lys43Arg (0.96)
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (1.00)
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.96 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
pncA 2289055 p.Asp63His missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 0.97 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.99 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
gyrB 6028 c.789C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8639 c.1338G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759608 c.-199C>T upstream_gene_variant 1.0
rpoB 759940 p.Pro45Leu missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.98
rplC 801066 c.258G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.22
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.32
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.42
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.42
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.3
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.3
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.26
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.24
rrl 1473924 n.267_268insT non_coding_transcript_exon_variant 0.24
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.22
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.23
rrl 1473981 n.324delGinsAT non_coding_transcript_exon_variant 0.18
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.21
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.19
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.2
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.24
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.23
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.27
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.25
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.27
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.33
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.21
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.11
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.25
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.19
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.15
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.16
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.14
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.14
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.16
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726323 p.Pro44Arg missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 0.99
Rv3083 3448598 p.Ile32Thr missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
rpoA 3878270 p.Leu80Val missense_variant 0.98
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268982 c.-146G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0