TB-Profiler result

Run: SRR26936949
Summary

Run ID: SRR26936949

Sample name:

Date: 06-02-2024 01:57:06

Number of reads: 4043813

Percentage reads mapped: 98.4

Strain: lineage2.2;lineage1.1.1.1

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 (0.62)
Isoniazid R katG p.Ser315Thr (0.49)
Ethambutol
Pyrazinamide R pncA p.Gly97Arg (0.32)
Streptomycin R rpsL p.Lys43Arg (0.39)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1401A>G (0.42)
Amikacin R rrs n.1401A>G (0.42)
Capreomycin R rrs n.1401A>G (0.42)
Kanamycin R rrs n.1401A>G (0.42)
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 0.43
lineage1 Indo-Oceanic EAI RD239 0.57
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.55
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.4
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.58
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO RD239 0.52
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 0.62 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.39 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.42 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.49 isoniazid
pncA 2288953 p.Gly97Arg missense_variant 0.32 pyrazinamide
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 6112 p.Met291Ile missense_variant 0.57
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.52
gyrA 8549 c.1248C>T synonymous_variant 0.6
gyrA 9143 c.1842T>C synonymous_variant 0.56
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490972 p.Arg64Ser missense_variant 0.64
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.39
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 0.35
rpoC 765171 p.Pro601Leu missense_variant 0.65
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.38
mmpL5 777581 p.Tyr300* stop_gained 0.63
mmpS5 779615 c.-710C>G upstream_gene_variant 0.44
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.37
Rv1258c 1407255 p.Ala29Val missense_variant 0.43
embR 1417019 p.Cys110Tyr missense_variant 0.41
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.59
rpsA 1834177 c.636A>C synonymous_variant 0.4
rpsA 1834319 p.Val260Ile missense_variant 0.61
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.55
Rv1979c 2222308 p.Asp286Gly missense_variant 0.53
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.53
kasA 2519267 p.Val385Ile missense_variant 0.58
eis 2714146 p.Val396Ala missense_variant 0.39
ahpC 2726051 c.-142G>A upstream_gene_variant 0.79
folC 2746885 c.714C>G synonymous_variant 0.37
Rv2752c 3064632 c.1560C>T synonymous_variant 0.53
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.59
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.72
fprA 3475159 p.Asn385Asp missense_variant 0.56
Rv3236c 3612813 p.Thr102Ala missense_variant 0.33
clpC1 4040517 p.Val63Ala missense_variant 0.61
embC 4240671 p.Thr270Ile missense_variant 0.69
embA 4243848 p.Val206Met missense_variant 0.61
embA 4244096 c.864C>T synonymous_variant 0.64
embA 4245969 p.Pro913Ser missense_variant 0.8
embB 4248195 p.Lys561Arg missense_variant 0.65
ubiA 4269387 p.Glu149Asp missense_variant 0.59
aftB 4269606 c.-770T>C upstream_gene_variant 0.56
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.62
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.59
gid 4407927 p.Glu92Asp missense_variant 0.44