TB-Profiler result

Run: ERR1034907
Summary

Run ID: ERR1034907

Sample name:

Date: 20-10-2023 23:25:16

Number of reads: 7066858

Percentage reads mapped: 98.08

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 (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Pro69Leu (1.00)
Streptomycin R gid p.Arg102* (0.99)
Fluoroquinolones R gyrB p.Ala504Val (0.92)
Moxifloxacin R gyrB p.Ala504Val (0.92)
Ofloxacin R gyrB p.Ala504Val (0.92)
Levofloxacin R gyrB p.Ala504Val (0.92)
Ciprofloxacin R gyrB p.Ala504Val (0.92)
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
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 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
gyrB 6750 p.Ala504Val missense_variant 0.92 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289036 p.Pro69Leu missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4407899 p.Arg102* stop_gained 0.99 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761998 p.Leu731Pro missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_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 1473752 n.95G>T non_coding_transcript_exon_variant 0.15
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.16
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.17
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.15
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.1
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.11
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.11
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.11
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.12
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.12
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.1
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.1
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.13
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.14
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.12
rrl 1475446 n.1789G>C non_coding_transcript_exon_variant 0.14
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.12
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.12
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.12
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.12
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.11
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.11
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.15
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.15
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.15
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.12
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714504 p.His277Tyr missense_variant 0.99
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039991 c.714G>A synonymous_variant 1.0
embC 4242159 p.Leu766Pro missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.99