TB-Profiler result

Run: ERR8975589

Summary

Run ID: ERR8975589

Sample name:

Date: 20-10-2023 16:04:14

Number of reads: 3149113

Percentage reads mapped: 99.61

Strain: lineage4.1.1.1;lineage2.2.1

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.His445Leu (0.37)
Isoniazid R fabG1 c.-8T>C (0.31), katG p.Thr394Ala (0.58), katG p.Ser315Thr (0.37)
Ethambutol R embB p.Met306Val (0.36)
Pyrazinamide R pncA c.439dupG (0.45)
Streptomycin R rpsL p.Lys43Arg (0.30)
Fluoroquinolones R gyrA p.Ala90Val (0.38)
Moxifloxacin R gyrA p.Ala90Val (0.38)
Ofloxacin R gyrA p.Ala90Val (0.38)
Levofloxacin R gyrA p.Ala90Val (0.38)
Ciprofloxacin R gyrA p.Ala90Val (0.38)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-8T>C (0.31)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.38
lineage4 Euro-American LAM;T;S;X;H None 0.65
lineage4.1 Euro-American T;X;H None 0.69
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.35
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.33
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.64
lineage4.1.1.1 Euro-American (X-type) X2 RD183 0.61
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 7570 p.Ala90Val missense_variant 0.38 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761140 p.His445Leu missense_variant 0.37 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.3 streptomycin
fabG1 1673432 c.-8T>C upstream_gene_variant 0.31 isoniazid, ethionamide
katG 2154932 p.Thr394Ala missense_variant 0.58 isoniazid
katG 2155168 p.Ser315Thr missense_variant 0.37 isoniazid
pncA 2288802 c.439dupG frameshift_variant 0.45 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.36 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.34
mshA 575907 p.Ala187Val missense_variant 0.37
ccsA 620625 p.Ile245Met missense_variant 0.34
rpoC 763031 c.-339T>C upstream_gene_variant 0.28
rpoC 765150 p.Gly594Glu missense_variant 0.76
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.34
mmpL5 776182 p.Asp767Asn missense_variant 0.41
mmpS5 779615 c.-710C>G upstream_gene_variant 0.35
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.35
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.31
PPE35 2167926 p.Leu896Ser missense_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726210 c.18T>C synonymous_variant 0.68
ald 3086739 c.-81G>A upstream_gene_variant 0.35
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.4
fbiA 3641447 p.Thr302Met missense_variant 0.69
rpoA 3877553 p.Glu319Lys missense_variant 0.73
embC 4240897 c.1035C>G synonymous_variant 0.63
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.6
embA 4243460 c.228C>T synonymous_variant 0.32
embB 4249408 c.2895G>A synonymous_variant 0.63
aftB 4267647 p.Asp397Gly missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.38
gid 4407927 p.Glu92Asp missense_variant 0.38