TB-Profiler result

Run: ERR9806866
Summary

Run ID: ERR9806866

Sample name:

Date: 18-05-2023 17:17:35

Number of reads: 2443162

Percentage reads mapped: 99.55

Strain: lineage4.1.1.3

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.Ile393Asn (0.13), katG p.Ser315Thr (1.00), ahpC c.-48G>A (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Val139Met (1.00)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrA p.Gly88Cys (1.00)
Moxifloxacin R gyrA p.Gly88Cys (1.00)
Ofloxacin R gyrA p.Gly88Cys (1.00)
Levofloxacin R gyrA p.Gly88Cys (1.00)
Ciprofloxacin R gyrA p.Gly88Cys (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.597delC (1.00), ethA c.597delC (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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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 7563 p.Gly88Cys missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2154934 p.Ile393Asn missense_variant 0.13 isoniazid
katG 2155167 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288827 p.Val139Met missense_variant 1.0 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326876 c.597delC frameshift_variant 1.0 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
gyrB 5701 c.466delC frameshift_variant 0.11
gyrB 6608 p.Val457Leu missense_variant 1.0
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 490780 c.-3C>A upstream_gene_variant 0.17
mshA 576469 c.1122G>T synonymous_variant 0.12
mshA 576590 p.Arg415Trp missense_variant 0.17
ccsA 619710 c.-181G>T upstream_gene_variant 0.15
rpoC 764744 c.1375C>A synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765842 p.Thr825Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777701 c.780C>T synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801354 c.546G>A synonymous_variant 1.0
fbiC 1304253 c.1323G>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154463 p.Ala550Val missense_variant 0.12
PPE35 2169900 p.Gly238Val missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065301 c.891C>A synonymous_variant 0.18
Rv2752c 3065364 c.828G>T synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338995 c.-123G>A upstream_gene_variant 0.14
fbiD 3339103 c.-15T>C upstream_gene_variant 0.18
Rv3083 3449616 p.Met371Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474652 c.648delC frameshift_variant 0.11
clpC1 4039405 p.Glu434* stop_gained 0.15
clpC1 4040307 c.397delC frameshift_variant 0.11
embC 4242072 p.Gly737Asp missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243494 p.Leu88Met missense_variant 0.12
embB 4247161 c.648G>A synonymous_variant 0.12
embB 4248705 p.Pro731Gln missense_variant 0.12
embB 4248717 p.Asn735Ser missense_variant 0.12
embB 4249041 p.Pro843Arg missense_variant 0.11
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267750 p.Phe363Leu missense_variant 0.11
aftB 4267878 p.Val320Gly missense_variant 0.33
aftB 4267938 p.Arg300Gln missense_variant 0.14
ubiA 4269760 p.Gln25Leu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0