TB-Profiler result

Run: SRR24256250
Summary

Run ID: SRR24256250

Sample name:

Date: 23-01-2024 02:40:05

Number of reads: 3811996

Percentage reads mapped: 99.66

Strain: lineage4.8;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 (0.39)
Isoniazid R katG p.Ser315Thr (0.44)
Ethambutol R embB p.Met306Ile (0.40)
Pyrazinamide R pncA p.Asp12Ala (0.42)
Streptomycin R rpsL p.Lys43Arg (0.37)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.884delT (0.28), ethA c.884delT (0.28)
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 0.37
lineage4 Euro-American LAM;T;S;X;H None 0.6
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.38
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.67
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.37
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 0.39 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.37 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.44 isoniazid
pncA 2289207 p.Asp12Ala missense_variant 0.42 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.4 ethambutol
ethA 4326589 c.884delT frameshift_variant 0.28 ethionamide, ethionamide
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 0.34
gyrA 9304 p.Gly668Asp missense_variant 0.41
fgd1 491742 c.960T>C synonymous_variant 0.42
mshA 575907 p.Ala187Val missense_variant 0.4
ccsA 620625 p.Ile245Met missense_variant 0.43
rpoB 761293 p.Val496Ala missense_variant 0.37
rpoC 763031 c.-339T>C upstream_gene_variant 0.34
rpoC 765369 p.Thr667Met missense_variant 0.63
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.38
mmpL5 776182 p.Asp767Asn missense_variant 0.35
mmpS5 779615 c.-710C>G upstream_gene_variant 0.34
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.37
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.53
rpsA 1834177 c.636A>C synonymous_variant 0.42
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.49
PPE35 2167926 p.Leu896Ser missense_variant 0.48
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 0.32
ald 3086788 c.-32T>C upstream_gene_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.41
Rv3236c 3612813 p.Thr102Ala missense_variant 0.34
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.29
embA 4243460 c.228C>T synonymous_variant 0.39
aftB 4267647 p.Asp397Gly missense_variant 0.33
whiB6 4338371 p.Thr51Pro missense_variant 0.34
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338630 c.-109C>A upstream_gene_variant 0.68
gid 4407588 c.615A>G synonymous_variant 0.39
gid 4407927 p.Glu92Asp missense_variant 0.38