TB-Profiler result

Run: SRR25827304
Summary

Run ID: SRR25827304

Sample name:

Date: 31-01-2024 22:03:11

Number of reads: 3258342

Percentage reads mapped: 95.27

Strain: lineage3.1.2;lineage2.2.1

Drug-resistance: 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 (0.63)
Isoniazid R katG p.Ser315Thr (0.47)
Ethambutol R embB p.Met306Val (0.53)
Pyrazinamide R pncA p.Thr177Pro (0.52)
Streptomycin R rpsL p.Lys43Arg (0.61)
Fluoroquinolones R gyrA p.Ala90Val (0.45), gyrA p.Asp94Gly (0.57)
Moxifloxacin R gyrA p.Ala90Val (0.45), gyrA p.Asp94Gly (0.57)
Ofloxacin R gyrA p.Ala90Val (0.45), gyrA p.Asp94Gly (0.57)
Levofloxacin R gyrA p.Ala90Val (0.45), gyrA p.Asp94Gly (0.57)
Ciprofloxacin R gyrA p.Ala90Val (0.45), gyrA p.Asp94Gly (0.57)
Aminoglycosides R rrs n.1401A>G (0.48)
Amikacin R rrs n.1401A>G (0.48)
Capreomycin R rrs n.1401A>G (0.48)
Kanamycin R rrs n.1401A>G (0.48)
Cycloserine R ald c.464delG (0.38)
Ethionamide R ethA c.774dupG (1.00), ethA c.774dupG (1.00)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.68)
Delamanid
Bedaquiline
Linezolid R rrl n.2814G>T (0.43)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.51
lineage2 East-Asian Beijing RD105 0.55
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.53
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.44
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.45
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.47
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 7570 p.Ala90Val missense_variant 0.45 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.57 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.63 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.61 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.48 kanamycin, capreomycin, aminoglycosides, amikacin
rrl 1476471 n.2814G>T non_coding_transcript_exon_variant 0.43 linezolid
katG 2155168 p.Ser315Thr missense_variant 0.47 isoniazid
pncA 2288713 p.Thr177Pro missense_variant 0.52 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.68 para-aminosalicylic_acid
ald 3087278 c.464delG frameshift_variant 0.38 cycloserine
embB 4247429 p.Met306Val missense_variant 0.53 ethambutol
ethA 4326699 c.774dupG frameshift_variant 1.0 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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.51
ccsA 620625 p.Ile245Met missense_variant 0.59
rpoB 759746 c.-61C>T upstream_gene_variant 0.53
rpoC 762434 c.-936T>G upstream_gene_variant 0.52
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764840 p.Ile491Val missense_variant 0.58
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.5
mmpS5 779615 c.-710C>G upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.46
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475250 n.1593C>A non_coding_transcript_exon_variant 0.61
rpsA 1834177 c.636A>C synonymous_variant 0.56
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 0.41
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.42
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.43
pncA 2289365 c.-125delC upstream_gene_variant 0.44
ahpC 2726105 c.-88G>A upstream_gene_variant 0.42
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086931 p.Gly38Ser missense_variant 0.55
Rv3083 3449354 c.852dupC frameshift_variant 0.53
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.57
embC 4239852 c.-11G>A upstream_gene_variant 0.49
embC 4241022 p.Ala387Val missense_variant 0.56
embC 4242075 p.Arg738Gln missense_variant 0.38
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.5
embA 4245835 p.Leu868Arg missense_variant 0.16
aftB 4267647 p.Asp397Gly missense_variant 0.42
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.63
gid 4407927 p.Glu92Asp missense_variant 0.61