TB-Profiler result

Run: SRR25827345
Summary

Run ID: SRR25827345

Sample name:

Date: 01-02-2024 01:55:40

Number of reads: 7957714

Percentage reads mapped: 98.71

Strain: lineage4.8;lineage3.1.2;lineage2.2.1;lineage1.1.2

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 (0.92)
Isoniazid R fabG1 c.-15C>T (0.41), katG p.Ser315Thr (0.68)
Ethambutol R embB p.Met306Val (0.32)
Pyrazinamide R pncA p.Gly132Ala (0.13), pncA p.Asp63Gly (0.21)
Streptomycin R rpsL p.Lys43Arg (0.45), gid p.Tyr22* (0.15)
Fluoroquinolones R gyrA p.Ala90Val (0.24), gyrA p.Asp94Gly (0.18)
Moxifloxacin R gyrA p.Ala90Val (0.24), gyrA p.Asp94Gly (0.18)
Ofloxacin R gyrA p.Ala90Val (0.24), gyrA p.Asp94Gly (0.18)
Levofloxacin R gyrA p.Ala90Val (0.24), gyrA p.Asp94Gly (0.18)
Ciprofloxacin R gyrA p.Ala90Val (0.24), gyrA p.Asp94Gly (0.18)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-37G>T (0.15)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.41)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.19)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.33
lineage2 East-Asian Beijing RD105 0.28
lineage4 Euro-American LAM;T;S;X;H None 0.18
lineage1 Indo-Oceanic EAI RD239 0.22
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.18
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.29
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.16
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.26
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.17
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.26
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.3
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 0.24 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.18 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.92 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.45 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.19 linezolid
fabG1 1673425 c.-15C>T upstream_gene_variant 0.41 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.68 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.13 pyrazinamide
pncA 2289054 p.Asp63Gly missense_variant 0.21 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 0.15 kanamycin
embB 4247429 p.Met306Val missense_variant 0.32 ethambutol
gid 4408137 p.Tyr22* stop_gained 0.15 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 5332 c.93C>T synonymous_variant 0.17
gyrB 6112 p.Met291Ile missense_variant 0.17
gyrB 6124 c.885C>T synonymous_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.81
gyrA 8168 p.Glu289Asp missense_variant 0.13
gyrA 8452 p.Ala384Val missense_variant 0.17
gyrA 9143 c.1842T>C synonymous_variant 0.21
gyrA 9304 p.Gly668Asp missense_variant 0.8
fgd1 491290 p.Val170Met missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 0.78
mshA 575907 p.Ala187Val missense_variant 0.31
ccsA 620553 c.663T>C synonymous_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 0.29
rpoB 759746 c.-61C>T upstream_gene_variant 0.34
rpoB 760490 c.684C>T synonymous_variant 0.22
rpoC 762434 c.-936T>G upstream_gene_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 0.76
rpoC 763884 p.Ala172Val missense_variant 0.17
rpoC 763886 c.517C>A synonymous_variant 0.17
rpoC 764363 p.Gly332Ser missense_variant 0.13
rpoC 764817 p.Val483Gly missense_variant 0.21
rpoC 764840 p.Ile491Val missense_variant 0.13
rpoC 765171 p.Pro601Leu missense_variant 0.19
rpoC 765862 p.Phe831Leu missense_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775964 c.2517G>C synonymous_variant 0.24
mmpL5 776100 p.Thr794Ile missense_variant 0.86
mmpL5 776182 p.Asp767Asn missense_variant 0.25
mmpL5 776395 p.Phe696Leu missense_variant 0.21
mmpR5 779243 p.Val85Gly missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 0.35
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801267 c.459A>G synonymous_variant 0.19
Rv1258c 1406760 c.580_581insC frameshift_variant 0.29
embR 1417019 p.Cys110Tyr missense_variant 0.21
atpE 1460890 c.-155G>T upstream_gene_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673406 c.-796C>G upstream_gene_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102791 c.252A>C synonymous_variant 0.2
katG 2153931 c.2181C>T synonymous_variant 0.26
katG 2154724 p.Arg463Leu missense_variant 0.87
PPE35 2167926 p.Leu896Ser missense_variant 0.86
PPE35 2167983 p.Gly877Asp missense_variant 0.22
PPE35 2168604 p.Pro670Leu missense_variant 0.24
PPE35 2170785 c.-173T>C upstream_gene_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 0.23
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 0.33
pncA 2289604 c.-363T>A upstream_gene_variant 0.25
kasA 2518132 c.18C>T synonymous_variant 0.2
eis 2715016 p.Arg106His missense_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 0.21
ahpC 2726105 c.-88G>A upstream_gene_variant 0.38
Rv2752c 3064632 c.1560C>T synonymous_variant 0.23
Rv2752c 3065419 p.Arg258Leu missense_variant 0.17
Rv2752c 3065773 p.Glu140Gly missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 0.84
ald 3086821 c.2T>G start_lost 0.16
Rv3083 3448714 p.Asp71His missense_variant 0.29
Rv3083 3448936 p.Tyr145Asp missense_variant 0.21
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.8
fprA 3474597 c.591C>A synonymous_variant 0.23
fprA 3475159 p.Asn385Asp missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 0.27
rpoA 3878575 c.-68C>A upstream_gene_variant 0.31
rpoA 3878641 c.-135delG upstream_gene_variant 0.16
clpC1 4040517 p.Val63Ala missense_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 0.27
embC 4241042 p.Asn394Asp missense_variant 0.24
embC 4242075 p.Arg738Gln missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.27
embA 4243848 p.Val206Met missense_variant 0.21
embA 4245417 p.Gly729Arg missense_variant 0.23
embA 4245969 p.Pro913Ser missense_variant 0.22
embB 4247028 p.Leu172Arg missense_variant 0.23
embB 4247646 p.Glu378Ala missense_variant 0.29
embB 4249485 p.Gly991Val missense_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 0.28
aftB 4269102 c.-266C>T upstream_gene_variant 0.2
ubiA 4269296 p.Met180Val missense_variant 0.16
ubiA 4269387 p.Glu149Asp missense_variant 0.21
aftB 4269606 c.-770T>C upstream_gene_variant 0.21
ethA 4326878 p.Ala199Asp missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.23
gid 4407588 c.615A>G synonymous_variant 0.87
gid 4407873 c.330G>T synonymous_variant 0.21
gid 4407927 p.Glu92Asp missense_variant 0.27