TB-Profiler result

Run: ERR12307397

Summary

Run ID: ERR12307397

Sample name:

Date: 09-01-2024 05:38:21

Number of reads: 11398346

Percentage reads mapped: 99.58

Strain: lineage4.8;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.Ser450Leu (0.53)
Isoniazid R katG p.Ser315Thr (0.51), katG p.Ser315Asn (0.49)
Ethambutol R embB p.Asp354Ala (0.53)
Pyrazinamide R pncA p.Asp63Ala (0.55)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrA p.Ala90Val (0.58)
Moxifloxacin R gyrA p.Ala90Val (0.58)
Ofloxacin R gyrA p.Ala90Val (0.58)
Levofloxacin R gyrA p.Ala90Val (0.58)
Ciprofloxacin R gyrA p.Ala90Val (0.58)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid R ddn p.Trp88* (0.59)
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.58
lineage4 Euro-American LAM;T;S;X;H None 0.45
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.57
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.46
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.56
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 0.58 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.53 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.51 isoniazid
katG 2155168 p.Ser315Asn missense_variant 0.49 isoniazid
pncA 2289054 p.Asp63Ala missense_variant 0.55 pyrazinamide
ddn 3987106 p.Trp88* stop_gained 0.59 delamanid
embB 4247574 p.Asp354Ala missense_variant 0.53 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 0.46
gyrA 9304 p.Gly668Asp missense_variant 0.53
fgd1 491742 c.960T>C synonymous_variant 0.58
mshA 575907 p.Ala187Val missense_variant 0.48
ccsA 620625 p.Ile245Met missense_variant 0.6
rpoC 763031 c.-339T>C upstream_gene_variant 0.61
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 0.53
mmpL5 776182 p.Asp767Asn missense_variant 0.62
mmpL5 778107 p.Ser125Cys missense_variant 0.41
mmpS5 779615 c.-710C>G upstream_gene_variant 0.56
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.63
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.38
rpsA 1834177 c.636A>C synonymous_variant 0.47
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.57
PPE35 2167926 p.Leu896Ser missense_variant 0.61
PPE35 2168149 p.Pro822Ser missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 0.58
ald 3086788 c.-32T>C upstream_gene_variant 0.63
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.52
Rv3236c 3612813 p.Thr102Ala missense_variant 0.61
rpoA 3877956 p.Glu184Asp missense_variant 0.51
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.52
embA 4243460 c.228C>T synonymous_variant 0.48
aftB 4267647 p.Asp397Gly missense_variant 0.54
ethA 4328378 c.-905G>C upstream_gene_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 0.57
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.57
gid 4407927 p.Glu92Asp missense_variant 0.51