TB-Profiler result

Run: ERR10610078
Summary

Run ID: ERR10610078

Sample name:

Date: 19-05-2023 07:49:59

Number of reads: 839050

Percentage reads mapped: 98.92

Strain: lineage4.1.2.1

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Asp435Val (0.18), rpoB p.Ser450Leu (0.88)
Isoniazid R katG p.Ser315Thr (1.00), ahpC c.-57C>T (0.95)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Thr135Pro (0.95)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.860delA (0.95), ethA c.860delA (0.95)
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 0.99
lineage4.1.2 Euro-American T;H None 0.96
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.97
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 761110 p.Asp435Val missense_variant 0.18 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.88 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288839 p.Thr135Pro missense_variant 0.95 pyrazinamide
ahpC 2726136 c.-57C>T upstream_gene_variant 0.95 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326613 c.860delA frameshift_variant 0.95 ethionamide, ethionamide
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 491382 p.Glu200Asp missense_variant 0.38
fgd1 491386 p.Leu202Ile missense_variant 0.29
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.17
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
rpoC 766488 p.Pro1040Arg 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
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.12
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.18
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.14
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.14
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519214 p.Ile367Ser missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878049 c.459G>C synonymous_variant 0.2
clpC1 4038444 p.Ala754Val missense_variant 0.12
clpC1 4038662 c.2043T>C synonymous_variant 0.14
clpC1 4039064 c.1641C>T synonymous_variant 0.15
clpC1 4039094 c.1611C>G synonymous_variant 0.14
clpC1 4039097 c.1608G>C synonymous_variant 0.13
clpC1 4039103 c.1602T>C synonymous_variant 0.15
clpC1 4039106 c.1599G>C synonymous_variant 0.14
clpC1 4039112 c.1593C>G synonymous_variant 0.13
clpC1 4039121 c.1584T>C synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0
whiB6 4338699 c.-179delT upstream_gene_variant 0.14
gid 4407927 p.Glu92Asp missense_variant 0.11