TB-Profiler result

Run: SRR5341261
Summary

Run ID: SRR5341261

Sample name:

Date: 21-10-2023 01:26:41

Number of reads: 1532827

Percentage reads mapped: 99.56

Strain: lineage4.2.2.2;lineage2.2.1

Drug-resistance: MDR-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 (0.49)
Isoniazid R katG p.Ser315Thr (0.31)
Ethambutol R embB p.Met306Ile (0.45)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.44), gid c.102delG (0.49)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
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 0.54
lineage4 Euro-American LAM;T;S;X;H None 0.45
lineage4.2 Euro-American H;T;LAM None 0.4
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.51
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.44
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.51
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.46
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
rpoB 761155 p.Ser450Leu missense_variant 0.49 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.44 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.31 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.45 ethambutol
gid 4408100 c.102delG frameshift_variant 0.49 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 5965 c.726A>G synonymous_variant 0.55
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8685 p.Ile462Val missense_variant 0.54
gyrA 8688 p.Ala463Ser missense_variant 0.44
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.44
mshA 575907 p.Ala187Val missense_variant 0.59
mshA 576077 c.730C>T synonymous_variant 0.35
ccsA 620625 p.Ile245Met missense_variant 0.55
rpoB 761489 c.1683G>A synonymous_variant 0.51
rpoC 763031 c.-339T>C upstream_gene_variant 0.6
rpoC 766485 p.Val1039Gly missense_variant 0.52
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.61
mmpL5 776182 p.Asp767Asn missense_variant 0.59
mmpS5 779615 c.-710C>G upstream_gene_variant 0.51
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305180 c.2250G>A synonymous_variant 0.49
Rv1258c 1406760 c.580_581insC frameshift_variant 0.42
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.44
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.49
PPE35 2167926 p.Leu896Ser missense_variant 0.75
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.45
thyX 3067467 p.Ala160Val missense_variant 0.64
thyX 3068145 c.-200C>A upstream_gene_variant 0.44
ald 3086742 c.-78A>C upstream_gene_variant 0.6
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 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.59
aftB 4267647 p.Asp397Gly missense_variant 0.48
whiB6 4338513 c.9C>T synonymous_variant 0.53
whiB6 4338595 c.-75delG upstream_gene_variant 0.91
gid 4407588 c.615A>G synonymous_variant 0.47
gid 4407927 p.Glu92Asp missense_variant 0.57