TB-Profiler result

Run: SRR25827581

Summary

Run ID: SRR25827581

Sample name:

Date: 02-02-2024 11:33:44

Number of reads: 25251799

Percentage reads mapped: 98.7

Strain: lineage2.2.1;lineage1.1.3.1

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 (0.68)
Isoniazid R katG p.Ser315Thr (0.66)
Ethambutol R embB p.Gln497Arg (0.66)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.68)
Fluoroquinolones R gyrA p.Asp94Gly (0.66)
Moxifloxacin R gyrA p.Asp94Gly (0.66)
Ofloxacin R gyrA p.Asp94Gly (0.66)
Levofloxacin R gyrA p.Asp94Gly (0.66)
Ciprofloxacin R gyrA p.Asp94Gly (0.66)
Aminoglycosides R rrs n.1401A>G (0.74)
Amikacin R rrs n.1401A>G (0.74)
Capreomycin R rrs n.1401A>G (0.74)
Kanamycin R rrs n.1401A>G (0.74)
Cycloserine
Ethionamide R ethA p.Cys294* (0.71)
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 0.71
lineage1 Indo-Oceanic EAI RD239 0.3
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.29
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.7
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.3
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.7
lineage1.1.3.1 Indo-Oceanic NA RD239 0.3
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.Asp94Gly missense_variant 0.66 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.68 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.68 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.74 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.66 isoniazid
embB 4248003 p.Gln497Arg missense_variant 0.66 ethambutol
ethA 4326592 p.Cys294* stop_gained 0.71 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
gyrB 6112 p.Met291Ile missense_variant 0.27
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.29
gyrA 9143 c.1842T>C synonymous_variant 0.26
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.71
ccsA 620625 p.Ile245Met missense_variant 0.7
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.31
rpoC 763886 c.517C>A synonymous_variant 0.31
rpoC 765171 p.Pro601Leu missense_variant 0.31
rpoC 765230 p.Ala621Thr missense_variant 0.34
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.73
mmpS5 779526 c.-621G>A upstream_gene_variant 0.34
mmpS5 779615 c.-710C>G upstream_gene_variant 0.69
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.71
embR 1417019 p.Cys110Tyr missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.69
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103068 c.-27_-26delAGinsC upstream_gene_variant 0.3
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.26
PPE35 2170048 p.Leu189Val missense_variant 0.19
PPE35 2170053 p.Thr187Ser missense_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.28
ahpC 2726051 c.-142G>A upstream_gene_variant 0.33
Rv2752c 3064632 c.1560C>T synonymous_variant 0.3
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.28
fprA 3475159 p.Asn385Asp missense_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 0.67
alr 3841253 c.168C>T synonymous_variant 0.26
clpC1 4040517 p.Val63Ala missense_variant 0.29
embC 4240671 p.Thr270Ile missense_variant 0.31
embC 4241022 p.Ala387Val missense_variant 0.7
embC 4241042 p.Asn394Asp missense_variant 0.31
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.71
embA 4243848 p.Val206Met missense_variant 0.33
embA 4245969 p.Pro913Ser missense_variant 0.31
embB 4246544 p.Thr11Pro missense_variant 0.38
embB 4246548 p.Pro12Gln missense_variant 0.37
embB 4246555 c.42G>C synonymous_variant 0.34
embB 4246556 p.Ala15Pro missense_variant 0.35
embB 4246563 p.Leu17Trp missense_variant 0.34
embB 4246567 c.54G>T synonymous_variant 0.3
embB 4247028 p.Leu172Arg missense_variant 0.2
embB 4247039 p.Phe176Val missense_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 0.3
aftB 4267647 p.Asp397Gly missense_variant 0.71
ubiA 4269387 p.Glu149Asp missense_variant 0.25
aftB 4269606 c.-770T>C upstream_gene_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.74
gid 4407780 c.423G>A synonymous_variant 0.28
gid 4407873 c.330G>T synonymous_variant 0.29
gid 4407927 p.Glu92Asp missense_variant 0.69
gid 4407998 p.Gly69Ser missense_variant 0.3