TB-Profiler result

Run: ERR4800367

Summary

Run ID: ERR4800367

Sample name:

Date: 20-10-2023 04:20:17

Number of reads: 3479858

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 (0.39)
Isoniazid R katG p.Ser315Thr (0.98)
Ethambutol R embB p.Met306Val (0.35)
Pyrazinamide R pncA p.Asp63Gly (0.26)
Streptomycin R rpsL p.Lys43Arg (0.33), rrs n.906A>G (0.77), gid c.102delG (0.77)
Fluoroquinolones R gyrA p.Ala90Val (0.28), gyrA p.Asp94Asn (0.64)
Moxifloxacin R gyrA p.Ala90Val (0.28), gyrA p.Asp94Asn (0.64)
Ofloxacin R gyrA p.Ala90Val (0.28), gyrA p.Asp94Asn (0.64)
Levofloxacin R gyrA p.Ala90Val (0.28), gyrA p.Asp94Asn (0.64)
Ciprofloxacin R gyrA p.Ala90Val (0.28), gyrA p.Asp94Asn (0.64)
Aminoglycosides R rrs n.1401A>G (0.23)
Amikacin R rrs n.1401A>G (0.23)
Capreomycin R rrs n.1401A>G (0.23)
Kanamycin R rrs n.1401A>G (0.23)
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
lineage2 East-Asian Beijing RD105 0.73
lineage4 Euro-American LAM;T;S;X;H None 0.3
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.68
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.29
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.66
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 0.28 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Asn missense_variant 0.64 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.39 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.33 streptomycin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.77 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.23 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2289054 p.Asp63Gly missense_variant 0.26 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.35 ethambutol
gid 4408100 c.102delG frameshift_variant 0.77 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
gyrB 5332 c.93C>T synonymous_variant 0.34
gyrA 7362 p.Glu21Gln missense_variant 0.99
gyrA 7585 p.Ser95Thr missense_variant 0.68
gyrA 8168 p.Glu289Asp missense_variant 0.3
gyrA 9304 p.Gly668Asp missense_variant 0.58
fgd1 491742 c.960T>C synonymous_variant 0.65
mshA 575907 p.Ala187Val missense_variant 0.77
ccsA 620625 p.Ile245Met missense_variant 0.72
rpoC 763031 c.-339T>C upstream_gene_variant 0.71
rpoC 765862 p.Phe831Leu missense_variant 0.35
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.69
mmpL5 776182 p.Asp767Asn missense_variant 0.68
mmpS5 779615 c.-710C>G upstream_gene_variant 0.7
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406738 c.603C>T synonymous_variant 0.72
Rv1258c 1406760 c.580_581insC frameshift_variant 0.68
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.2
inhA 1673406 c.-796C>G upstream_gene_variant 0.31
rpsA 1834177 c.636A>C synonymous_variant 0.61
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.62
PPE35 2167926 p.Leu896Ser missense_variant 0.73
PPE35 2168149 p.Pro822Ser missense_variant 0.26
PPE35 2169424 p.Ser397Pro missense_variant 0.71
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747470 p.Ile43Ala missense_variant 0.29
Rv2752c 3065773 p.Glu140Gly missense_variant 0.33
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.64
ald 3086788 c.-32T>C upstream_gene_variant 0.71
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.69
Rv3236c 3612813 p.Thr102Ala missense_variant 0.65
clpC1 4039729 p.Asp326Asn missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.74
embA 4245417 p.Gly729Arg missense_variant 0.4
embB 4249109 p.Pro866Thr missense_variant 0.77
aftB 4267647 p.Asp397Gly missense_variant 0.73
ubiA 4269296 p.Met180Val missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.71
gid 4407927 p.Glu92Asp missense_variant 0.71