TB-Profiler result

Run: SRR25827614
Summary

Run ID: SRR25827614

Sample name:

Date: 15-03-2024 21:08:12

Number of reads: 2297904

Percentage reads mapped: 99.13

Strain: lineage4.9;lineage3;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.Val170Phe (0.34), rpoB p.Ser450Leu (0.40)
Isoniazid R fabG1 c.-15C>T (0.14), katG p.Ser315Thr (0.60)
Ethambutol R embB p.Met306Val (0.35)
Pyrazinamide R pncA p.Gly132Ala (0.16)
Streptomycin R rpsL p.Lys43Arg (0.41)
Fluoroquinolones R gyrA p.Ala90Val (0.28), gyrA p.Asp94Gly (0.52)
Moxifloxacin R gyrA p.Ala90Val (0.28), gyrA p.Asp94Gly (0.52)
Ofloxacin R gyrA p.Ala90Val (0.28), gyrA p.Asp94Gly (0.52)
Levofloxacin R gyrA p.Ala90Val (0.28), gyrA p.Asp94Gly (0.52)
Ciprofloxacin R gyrA p.Ala90Val (0.28), gyrA p.Asp94Gly (0.52)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.14)
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 0.09
lineage2 East-Asian Beijing RD105 0.39
lineage4 Euro-American LAM;T;S;X;H None 0.19
lineage1 Indo-Oceanic EAI RD239 0.27
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.38
lineage4.9 Euro-American (H37Rv-like) T1 None 0.12
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.3
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.37
lineage1.2.2.2 Indo-Oceanic NA RD239 0.22
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 0.28 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.52 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 760314 p.Val170Phe missense_variant 0.34 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.4 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.41 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.14 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.6 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.16 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.35 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 0.33
gyrB 6112 p.Met291Ile missense_variant 0.31
gyrB 6184 c.945C>T synonymous_variant 0.38
gyrA 7268 c.-34C>T upstream_gene_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 0.87
gyrA 7585 p.Ser95Thr missense_variant 0.84
gyrA 7943 p.Glu214Asp missense_variant 0.27
gyrA 8452 p.Ala384Val missense_variant 0.28
gyrA 9143 c.1842T>C synonymous_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 0.76
fgd1 491290 p.Val170Met missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 0.72
mshA 575907 p.Ala187Val missense_variant 0.44
ccsA 620625 p.Ile245Met missense_variant 0.34
rpoC 762434 c.-936T>G upstream_gene_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 0.79
rpoC 763884 p.Ala172Val missense_variant 0.29
rpoC 763886 c.517C>A synonymous_variant 0.29
rpoC 764840 p.Ile491Val missense_variant 0.13
rpoC 765863 p.Ile832Val missense_variant 0.31
mmpL5 775639 p.Ile948Val missense_variant 0.83
mmpL5 776100 p.Thr794Ile missense_variant 0.9
mmpL5 776182 p.Asp767Asn missense_variant 0.46
mmpS5 779615 c.-710C>G upstream_gene_variant 0.36
rpsL 781395 c.-165T>C upstream_gene_variant 0.83
Rv1258c 1406760 c.580_581insC frameshift_variant 0.46
embR 1417019 p.Cys110Tyr missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 0.95
rpsA 1834177 c.636A>C synonymous_variant 0.47
tlyA 1917972 c.33A>G synonymous_variant 0.88
katG 2154724 p.Arg463Leu missense_variant 0.76
PPE35 2167926 p.Leu896Ser missense_variant 0.88
PPE35 2168742 p.Gly624Asp missense_variant 0.29
Rv1979c 2222308 p.Asp286Gly missense_variant 0.35
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.88
kasA 2518132 c.18C>T synonymous_variant 0.36
ahpC 2726051 c.-142G>A upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 0.86
Rv3083 3448714 p.Asp71His missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.81
fprA 3474597 c.591C>A synonymous_variant 0.29
fprA 3475159 p.Asn385Asp missense_variant 0.23
Rv3236c 3612813 p.Thr102Ala missense_variant 0.35
clpC1 4038425 c.2280C>T synonymous_variant 0.32
clpC1 4040517 p.Val63Ala missense_variant 0.27
embC 4240671 p.Thr270Ile missense_variant 0.21
embC 4241022 p.Ala387Val missense_variant 0.19
embC 4241042 p.Asn394Asp missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 0.89
embA 4243460 c.228C>T synonymous_variant 0.4
embA 4244061 p.Leu277Phe missense_variant 0.26
embA 4245969 p.Pro913Ser missense_variant 0.26
embB 4247646 p.Glu378Ala missense_variant 0.28
aftB 4267647 p.Asp397Gly missense_variant 0.28
ubiA 4269387 p.Glu149Asp missense_variant 0.28
aftB 4269606 c.-770T>C upstream_gene_variant 0.28
ethA 4326148 c.1326G>T synonymous_variant 0.32
ethA 4326439 p.Asn345Lys missense_variant 0.25
whiB6 4338203 p.Arg107Cys missense_variant 0.35
whiB6 4338595 c.-75delG upstream_gene_variant 0.91
whiB6 4338603 c.-82C>T upstream_gene_variant 0.32
gid 4407588 c.615A>G synonymous_variant 0.82
gid 4407620 p.Tyr195His missense_variant 0.18
gid 4407873 c.330G>T synonymous_variant 0.31
gid 4407927 p.Glu92Asp missense_variant 0.36