TB-Profiler result

Run: ERR2706923
Summary

Run ID: ERR2706923

Sample name:

Date: 19-10-2023 12:10:00

Number of reads: 3631908

Percentage reads mapped: 99.54

Strain: lineage4.3.3;lineage4.1.2;lineage4.1.1.1

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
Rifampicin R rpoB p.Leu452Pro (0.32)
Isoniazid R katG p.Ser315Thr (0.31)
Ethambutol R embB p.Met306Ile (0.33)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.28)
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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.33
lineage4.1 Euro-American T;X;H None 0.7
lineage4.1.2 Euro-American T;H None 0.22
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.47
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.31
lineage4.1.1.1 Euro-American (X-type) X2 RD183 0.45
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 761161 p.Leu452Pro missense_variant 0.32 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.28 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.31 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.33 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 8040 p.Gly247Ser missense_variant 0.3
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491616 p.Glu278Asp missense_variant 0.35
rpoC 764995 c.1626C>G synonymous_variant 0.26
rpoC 765150 p.Gly594Glu missense_variant 0.65
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776417 c.2064G>A synonymous_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781676 c.117C>T synonymous_variant 0.32
embR 1417140 p.Ala70Ser missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476055 n.2398C>T non_coding_transcript_exon_variant 0.38
fabG1 1673249 c.-191C>T upstream_gene_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.27
ahpC 2726210 c.18T>C synonymous_variant 0.46
folC 2747022 p.Val193Ile missense_variant 0.12
folC 2747044 c.555C>T synonymous_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339550 p.Gly145Arg missense_variant 0.47
Rv3083 3448894 p.Tyr131Asp missense_variant 0.23
Rv3083 3449642 p.Asn380Ser missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641164 p.Ile208Val missense_variant 0.23
fbiA 3641447 p.Thr302Met missense_variant 0.57
rpoA 3877553 p.Glu319Lys missense_variant 0.5
clpC1 4038287 c.2418C>T synonymous_variant 0.35
embC 4240897 c.1035C>G synonymous_variant 0.47
embC 4242182 p.Ala774Ser missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.73
embB 4249408 c.2895G>A synonymous_variant 0.51
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.28