TB-Profiler result

Run: SRR24710070
Summary

Run ID: SRR24710070

Sample name:

Date: 03-03-2024 08:26:40

Number of reads: 5533657

Percentage reads mapped: 99.4

Strain: lineage4.3.3;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 (0.34)
Isoniazid R fabG1 c.-15C>T (0.76), katG p.Ser315Thr (0.99)
Ethambutol R embB p.Met306Val (0.30)
Pyrazinamide R pncA p.Leu4Trp (0.27)
Streptomycin R rpsL p.Lys43Arg (0.21), rrs n.514A>C (0.84)
Fluoroquinolones R gyrA p.Asp94Ala (0.17)
Moxifloxacin R gyrA p.Asp94Ala (0.17)
Ofloxacin R gyrA p.Asp94Ala (0.17)
Levofloxacin R gyrA p.Asp94Ala (0.17)
Ciprofloxacin R gyrA p.Asp94Ala (0.17)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.76)
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 0.26
lineage4 Euro-American LAM;T;S;X;H None 0.73
lineage4.3 Euro-American (LAM) mainly-LAM None 0.75
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.26
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.23
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.75
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 7582 p.Asp94Ala missense_variant 0.17 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.34 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.21 streptomycin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.84 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.76 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289231 p.Leu4Trp missense_variant 0.27 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.3 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 8040 p.Gly247Ser missense_variant 0.75
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.24
mshA 575907 p.Ala187Val missense_variant 0.23
ccsA 620625 p.Ile245Met missense_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 0.23
rpoC 764714 p.Leu449Val missense_variant 0.26
rpoC 764995 c.1626C>G synonymous_variant 0.75
rpoC 766645 p.Glu1092Asp missense_variant 0.3
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.23
mmpL5 776182 p.Asp767Asn missense_variant 0.23
mmpS5 779615 c.-710C>G upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.71
fbiC 1304962 p.Trp678Gly missense_variant 0.82
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.25
rpsA 1834836 p.Met432Thr missense_variant 0.72
tlyA 1917972 c.33A>G synonymous_variant 0.99
katG 2154724 p.Arg463Leu missense_variant 0.23
katG 2156196 c.-85C>T upstream_gene_variant 0.78
PPE35 2167926 p.Leu896Ser missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.71
folC 2746340 p.Ala420Val missense_variant 0.65
ribD 2986827 c.-12G>A upstream_gene_variant 0.79
thyA 3073715 p.Pro253Ala missense_variant 0.29
thyA 3073868 p.Thr202Ala missense_variant 0.7
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 0.24
clpC1 4038287 c.2418C>T synonymous_variant 0.72
clpC1 4038968 c.1737G>A synonymous_variant 0.73
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.32
embB 4248634 c.2121A>G synonymous_variant 0.78
ethA 4326533 p.Thr314Ile missense_variant 0.2
ethA 4326983 p.Pro164Leu missense_variant 0.76
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.28
gid 4407927 p.Glu92Asp missense_variant 0.25
gid 4408156 p.Leu16Arg missense_variant 0.79