TB-Profiler result

Run: SRR25827457
Summary

Run ID: SRR25827457

Sample name:

Date: 21-03-2024 08:55:14

Number of reads: 9892147

Percentage reads mapped: 98.82

Strain: lineage3;lineage1.2.2.2

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.Asp435Val (0.30), rpoB p.Ser450Leu (0.70)
Isoniazid R katG c.1284delG (0.32), katG c.1284delG (0.32), katG p.Ser315Thr (0.68)
Ethambutol R embB p.Asp1024Asn (0.29)
Pyrazinamide R pncA p.Arg154Gly (0.33), pncA p.Phe13Ser (0.66)
Streptomycin R rrs n.905C>A (0.36), gid c.115delC (0.71)
Fluoroquinolones R gyrA p.Asp94Asn (0.27)
Moxifloxacin R gyrA p.Asp94Asn (0.27)
Ofloxacin R gyrA p.Asp94Asn (0.27)
Levofloxacin R gyrA p.Asp94Asn (0.27)
Ciprofloxacin R gyrA p.Asp94Asn (0.27)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
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
lineage3 East-African-Indian CAS RD750 0.32
lineage1 Indo-Oceanic EAI RD239 0.66
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.67
lineage1.2.2.2 Indo-Oceanic NA RD239 0.68
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 0.27 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.3 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.7 rifampicin
rrs 1472750 n.905C>A non_coding_transcript_exon_variant 0.36 streptomycin
katG 2154827 c.1284delG frameshift_variant 0.32 isoniazid, isoniazid
katG 2155168 p.Ser315Thr missense_variant 0.68 isoniazid
pncA 2288782 p.Arg154Gly missense_variant 0.33 pyrazinamide
pncA 2289204 p.Phe13Ser missense_variant 0.66 pyrazinamide
embB 4249583 p.Asp1024Asn missense_variant 0.29 ethambutol
gid 4408087 c.115delC frameshift_variant 0.71 streptomycin
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 5075 c.-165C>T upstream_gene_variant 0.68
gyrB 6112 p.Met291Ile missense_variant 0.68
gyrA 7268 c.-34C>T upstream_gene_variant 0.7
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.7
gyrA 9143 c.1842T>C synonymous_variant 0.66
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491103 c.321C>T synonymous_variant 0.21
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.35
rpoC 762434 c.-936T>G upstream_gene_variant 0.32
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.67
rpoC 763886 c.517C>A synonymous_variant 0.68
rpoC 764840 p.Ile491Val missense_variant 0.63
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776967 p.Gly505Asp missense_variant 0.65
mmpS5 779625 c.-720G>A upstream_gene_variant 0.65
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.7
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 0.7
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156557 c.-446G>T upstream_gene_variant 0.31
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.64
Rv1979c 2222308 p.Asp286Gly missense_variant 0.68
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.3
pncA 2289365 c.-125delC upstream_gene_variant 0.31
kasA 2518132 c.18C>T synonymous_variant 0.66
ahpC 2726051 c.-142G>A upstream_gene_variant 0.68
ahpC 2726105 c.-88G>A upstream_gene_variant 0.37
ahpC 2726117 c.-76T>G upstream_gene_variant 0.3
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.63
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.64
fprA 3475159 p.Asn385Asp missense_variant 0.63
alr 3840419 c.1002A>G synonymous_variant 0.69
clpC1 4040517 p.Val63Ala missense_variant 0.68
clpC1 4040719 c.-15A>G upstream_gene_variant 0.68
embC 4240671 p.Thr270Ile missense_variant 0.65
embC 4241042 p.Asn394Asp missense_variant 0.67
embC 4242075 p.Arg738Gln missense_variant 0.31
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 0.61
embA 4243217 c.-16C>A upstream_gene_variant 0.41
embA 4245969 p.Pro913Ser missense_variant 0.67
embB 4247502 p.Phe330Ser missense_variant 0.69
embB 4247646 p.Glu378Ala missense_variant 0.68
aftB 4267960 p.Val293Met missense_variant 0.68
ubiA 4269387 p.Glu149Asp missense_variant 0.64
aftB 4269606 c.-770T>C upstream_gene_variant 0.64
ethA 4326148 c.1326G>T synonymous_variant 0.63
ethA 4326439 p.Asn345Lys missense_variant 0.66
whiB6 4338203 p.Arg107Cys missense_variant 0.72
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.64
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407848 p.Ala119Thr missense_variant 0.68
gid 4407873 c.330G>T synonymous_variant 0.66