TB-Profiler result

Run: ERR4799582
Summary

Run ID: ERR4799582

Sample name:

Date: 20-10-2023 03:41:05

Number of reads: 3297705

Percentage reads mapped: 99.6

Strain: 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 (1.00)
Isoniazid R fabG1 c.-15C>T (0.98), katG p.Ser315Thr (0.99)
Ethambutol R embA c.-11C>A (0.95), embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Leu27Pro (0.97)
Streptomycin R rpsL p.Lys43Arg (0.99)
Fluoroquinolones R gyrB p.Thr500Asn (0.38), gyrA p.Ala90Val (0.94), gyrA p.Asp94Gly (0.41)
Moxifloxacin R gyrB p.Thr500Asn (0.38), gyrA p.Ala90Val (0.94), gyrA p.Asp94Gly (0.41)
Ofloxacin R gyrB p.Thr500Asn (0.38), gyrA p.Ala90Val (0.94), gyrA p.Asp94Gly (0.41)
Levofloxacin R gyrB p.Thr500Asn (0.38), gyrA p.Ala90Val (0.94), gyrA p.Asp94Gly (0.41)
Ciprofloxacin R gyrB p.Thr500Asn (0.38), gyrA p.Ala90Val (0.94), gyrA p.Asp94Gly (0.41)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine R ald c.464delG (0.32)
Ethionamide R fabG1 c.-15C>T (0.98)
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 0.98
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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 6738 p.Thr500Asn missense_variant 0.38 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 0.94 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.41 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.98 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 0.97 pyrazinamide
ald 3087278 c.464delG frameshift_variant 0.32 cycloserine
embA 4243222 c.-11C>A upstream_gene_variant 0.95 ethambutol
embB 4247429 p.Met306Val missense_variant 1.0 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 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766488 p.Pro1040Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086846 c.32delA frameshift_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568487 c.192dupC frameshift_variant 1.0
whiB7 3568854 c.-176delG upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.99
aftB 4267647 p.Asp397Gly missense_variant 0.96
ethA 4326513 p.Thr321Pro missense_variant 0.98
ethA 4326676 p.Ser266Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.98