TB-Profiler result

Run: SRR25827357

Summary

Run ID: SRR25827357

Sample name:

Date: 01-02-2024 03:07:32

Number of reads: 11680898

Percentage reads mapped: 99.05

Strain: lineage3;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 (0.61), rpoB p.Ile480Val (0.45), rpoB p.Ile491Phe (0.41)
Isoniazid R katG p.Ser315Thr (0.99)
Ethambutol R embB p.Met306Val (0.17), embB p.Gln497Arg (0.50)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.41), rpsL p.Lys88Thr (0.18)
Fluoroquinolones R gyrB p.Thr500Asn (0.42), gyrA p.Ser91Pro (0.15)
Moxifloxacin R gyrB p.Thr500Asn (0.42), gyrA p.Ser91Pro (0.15)
Ofloxacin R gyrB p.Thr500Asn (0.42), gyrA p.Ser91Pro (0.15)
Levofloxacin R gyrB p.Thr500Asn (0.42), gyrA p.Ser91Pro (0.15)
Ciprofloxacin R gyrB p.Thr500Asn (0.42), gyrA p.Ser91Pro (0.15)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-10G>A (0.46)
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.38)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.15
lineage2 East-Asian Beijing RD105 0.28
lineage1 Indo-Oceanic EAI RD239 0.43
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.43
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.3
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.43
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.26
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
gyrB 6738 p.Thr500Asn missense_variant 0.42 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.15 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.61 rifampicin
rpoB 761244 p.Ile480Val missense_variant 0.45 rifampicin
rpoB 761277 p.Ile491Phe missense_variant 0.41 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.41 streptomycin
rpsL 781822 p.Lys88Thr missense_variant 0.18 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.38 linezolid
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
eis 2715342 c.-10G>A upstream_gene_variant 0.46 kanamycin
embB 4247429 p.Met306Val missense_variant 0.17 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.5 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 6112 p.Met291Ile missense_variant 0.43
gyrB 6124 c.885C>T synonymous_variant 0.43
gyrA 6736 c.-566C>T upstream_gene_variant 0.42
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.45
gyrA 9143 c.1842T>C synonymous_variant 0.42
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 0.9
mshA 575907 p.Ala187Val missense_variant 0.24
ccsA 620553 c.663T>C synonymous_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 0.32
rpoB 759746 c.-61C>T upstream_gene_variant 0.17
rpoC 762434 c.-936T>G upstream_gene_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.87
rpoC 763884 p.Ala172Val missense_variant 0.37
rpoC 763886 c.517C>A synonymous_variant 0.37
rpoC 764817 p.Val483Ala missense_variant 0.13
rpoC 765171 p.Pro601Leu missense_variant 0.46
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.86
mmpL5 776182 p.Asp767Asn missense_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 0.28
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406503 p.Val280Leu missense_variant 0.42
Rv1258c 1406760 c.580_581insC frameshift_variant 0.27
embR 1417019 p.Cys110Tyr missense_variant 0.45
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102072 c.969_970dupGG frameshift_variant 0.37
katG 2154724 p.Arg463Leu missense_variant 0.84
PPE35 2167926 p.Leu896Ser missense_variant 0.85
PPE35 2167983 p.Gly877Asp missense_variant 0.38
PPE35 2168565 p.Pro683Leu missense_variant 0.16
PPE35 2170599 p.Val5Ala missense_variant 0.19
Rv1979c 2222308 p.Asp286Gly missense_variant 0.38
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.18
pncA 2289082 p.Pro54Ser missense_variant 0.42
pncA 2289365 c.-125delC upstream_gene_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 0.54
ahpC 2726051 c.-142G>A upstream_gene_variant 0.39
ribD 2986827 c.-12G>A upstream_gene_variant 0.27
Rv2752c 3064632 c.1560C>T synonymous_variant 0.42
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.44
fprA 3475159 p.Asn385Asp missense_variant 0.42
whiB7 3568425 c.255T>G synonymous_variant 0.16
Rv3236c 3612813 p.Thr102Ala missense_variant 0.29
clpC1 4040517 p.Val63Ala missense_variant 0.49
embC 4240671 p.Thr270Ile missense_variant 0.47
embC 4241022 p.Ala387Val missense_variant 0.19
embC 4241042 p.Asn394Asp missense_variant 0.37
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 0.44
embA 4245969 p.Pro913Ser missense_variant 0.4
embB 4246563 p.Leu17Trp missense_variant 0.54
embB 4246567 c.54G>T synonymous_variant 0.59
embB 4247028 p.Leu172Arg missense_variant 0.15
embB 4247646 p.Glu378Ala missense_variant 0.42
aftB 4267647 p.Asp397Gly missense_variant 0.21
ubiA 4269387 p.Glu149Asp missense_variant 0.45
aftB 4269606 c.-770T>C upstream_gene_variant 0.4
whiB6 4338224 c.297delC frameshift_variant 0.43
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.39
gid 4407588 c.615A>G synonymous_variant 0.88
gid 4407714 p.Lys163Asn missense_variant 0.48
gid 4407873 c.330G>T synonymous_variant 0.43
gid 4407927 p.Glu92Asp missense_variant 0.3