TB-Profiler result

Run: SRR25827375
Summary

Run ID: SRR25827375

Sample name:

Date: 01-02-2024 05:18:30

Number of reads: 7948425

Percentage reads mapped: 98.32

Strain: lineage2.2.1;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.Ser450Leu (0.26)
Isoniazid R katG p.Ser315Thr (0.30), ahpC p.Glu76Lys (0.61)
Ethambutol R embB p.Met306Val (0.20), embB p.Gln853Pro (0.24)
Pyrazinamide R pncA p.Asp63Ala (0.17)
Streptomycin R rpsL p.Lys43Arg (0.20)
Fluoroquinolones R gyrA p.Asp94Tyr (0.19)
Moxifloxacin R gyrA p.Asp94Tyr (0.19)
Ofloxacin R gyrA p.Asp94Tyr (0.19)
Levofloxacin R gyrA p.Asp94Tyr (0.19)
Ciprofloxacin R gyrA p.Asp94Tyr (0.19)
Aminoglycosides R rrs n.1401A>G (0.15)
Amikacin R rrs n.1401A>G (0.15)
Capreomycin R rrs n.1401A>G (0.15)
Kanamycin R rrs n.1401A>G (0.15)
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.33)
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 0.21
lineage1 Indo-Oceanic EAI RD239 0.8
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.21
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.68
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.19
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.Asp94Tyr missense_variant 0.19 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.26 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.2 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.15 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.3 isoniazid
pncA 2289054 p.Asp63Ala missense_variant 0.17 pyrazinamide
ahpC 2726418 p.Glu76Lys missense_variant 0.61 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 0.33 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.2 ethambutol
embB 4249071 p.Gln853Pro missense_variant 0.24 ethambutol
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 0.7
gyrB 6112 p.Met291Ile missense_variant 0.77
gyrA 7268 c.-34C>T upstream_gene_variant 0.71
gyrA 7283 c.-19G>T upstream_gene_variant 0.21
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.79
gyrA 9143 c.1842T>C synonymous_variant 0.82
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.19
ccsA 620625 p.Ile245Met missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.82
rpoC 763886 c.517C>A synonymous_variant 0.81
rpoC 764666 p.Gly433Ser missense_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 0.22
mmpS5 779625 c.-720G>A upstream_gene_variant 0.67
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.21
embR 1417019 p.Cys110Tyr missense_variant 0.75
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 0.71
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.62
Rv1979c 2222159 c.1006C>T synonymous_variant 0.76
Rv1979c 2222308 p.Asp286Gly missense_variant 0.78
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.77
ahpC 2726051 c.-142G>A upstream_gene_variant 0.77
pepQ 2860365 c.54G>T synonymous_variant 0.22
thyA 3074069 p.Val135Phe missense_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.75
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.8
fprA 3475159 p.Asn385Asp missense_variant 0.83
Rv3236c 3612813 p.Thr102Ala missense_variant 0.24
clpC1 4040517 p.Val63Ala missense_variant 0.75
clpC1 4040719 c.-15A>G upstream_gene_variant 0.68
embC 4240671 p.Thr270Ile missense_variant 0.81
embC 4241042 p.Asn394Asp missense_variant 0.73
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 0.21
embA 4243460 c.228C>T synonymous_variant 0.18
embA 4245835 p.Leu868Arg missense_variant 0.15
embA 4245969 p.Pro913Ser missense_variant 0.76
embB 4247015 p.Ser168Ala missense_variant 0.21
embB 4247646 p.Glu378Ala missense_variant 0.82
embB 4249757 p.Thr1082Ala missense_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 0.17
aftB 4267960 p.Val293Met missense_variant 0.74
ubiA 4269387 p.Glu149Asp missense_variant 0.78
aftB 4269606 c.-770T>C upstream_gene_variant 0.79
ethA 4326148 c.1326G>T synonymous_variant 0.69
ethA 4326439 p.Asn345Lys missense_variant 0.75
whiB6 4338203 p.Arg107Cys missense_variant 0.86
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.8
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407848 p.Ala119Thr missense_variant 0.69
gid 4407873 c.330G>T synonymous_variant 0.83
gid 4407927 p.Glu92Asp missense_variant 0.17