TB-Profiler result

Run: ERR4797638
Summary

Run ID: ERR4797638

Sample name:

Date: 20-10-2023 02:34:17

Number of reads: 3759012

Percentage reads mapped: 99.65

Strain: lineage3.1.2;lineage2.2.1

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 (0.98)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.26), embB p.Gln497Arg (0.72)
Pyrazinamide R pncA p.Cys138Arg (0.79), pncA c.192_193insA (0.32), pncA c.192_193insA (0.32)
Streptomycin R rpsL p.Lys43Arg (0.75), rrs n.514A>C (0.29)
Fluoroquinolones R gyrA p.Asp94Asn (0.65)
Moxifloxacin R gyrA p.Asp94Asn (0.65)
Ofloxacin R gyrA p.Asp94Asn (0.65)
Levofloxacin R gyrA p.Asp94Asn (0.65)
Ciprofloxacin R gyrA p.Asp94Asn (0.65)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA p.Pro378Leu (0.30), ethA p.Ser57Tyr (0.74)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.27
lineage2 East-Asian Beijing RD105 0.71
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.73
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.32
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.3
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.73
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 7581 p.Asp94Asn missense_variant 0.65 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.75 streptomycin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.29 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288830 p.Cys138Arg missense_variant 0.79 pyrazinamide
pncA 2289049 c.192_193insA frameshift_variant 0.32 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.26 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.72 ethambutol
ethA 4326341 p.Pro378Leu missense_variant 0.3 ethionamide
ethA 4327304 p.Ser57Tyr missense_variant 0.74 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 491290 p.Val170Met missense_variant 0.7
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.78
ccsA 620625 p.Ile245Met missense_variant 0.68
rpoB 759746 c.-61C>T upstream_gene_variant 0.25
rpoC 762434 c.-936T>G upstream_gene_variant 0.31
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764533 c.1164C>A synonymous_variant 0.74
rpoC 764840 p.Ile491Val missense_variant 0.73
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.71
mmpL5 776585 c.1896C>T synonymous_variant 0.33
mmpS5 779615 c.-710C>G upstream_gene_variant 0.75
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406242 p.Ala367Thr missense_variant 0.21
Rv1258c 1406760 c.580_581insC frameshift_variant 0.72
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.71
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 0.31
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.31
pncA 2289365 c.-125delC upstream_gene_variant 0.25
ahpC 2726105 c.-88G>A upstream_gene_variant 0.36
thyA 3074495 c.-24C>T upstream_gene_variant 0.25
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 0.75
embC 4241022 p.Ala387Val missense_variant 0.73
embC 4242075 p.Arg738Gln missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.69
aftB 4267647 p.Asp397Gly missense_variant 0.78
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.68
gid 4407892 p.Met104Lys missense_variant 0.34
gid 4407927 p.Glu92Asp missense_variant 0.72