TB-Profiler result

Run: SRR25827875
Summary

Run ID: SRR25827875

Sample name:

Date: 03-02-2024 00:02:34

Number of reads: 8393187

Percentage reads mapped: 99.25

Strain: 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.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (0.35), inhA p.Ile194Thr (0.21), katG p.Ser315Thr (0.84)
Ethambutol R embB p.Met306Val (0.23), embB p.Gly406Ser (0.23), embB p.Gln497Arg (0.25)
Pyrazinamide R pncA p.Arg154Gly (0.20), pncA p.Gly132Ala (0.24), pncA p.Leu27Pro (0.18), pncA p.Asp12Glu (0.43)
Streptomycin R rpsL p.Lys43Arg (0.32)
Fluoroquinolones R gyrA p.Ala90Val (0.15)
Moxifloxacin R gyrA p.Ala90Val (0.15)
Ofloxacin R gyrA p.Ala90Val (0.15)
Levofloxacin R gyrA p.Ala90Val (0.15)
Ciprofloxacin R gyrA p.Ala90Val (0.15)
Aminoglycosides R rrs n.1401A>G (0.41)
Amikacin R rrs n.1401A>G (0.41)
Capreomycin R rrs n.1401A>G (0.41)
Kanamycin R rrs n.1401A>G (0.41)
Cycloserine R ald c.436_437dupGC (0.14)
Ethionamide R fabG1 c.-15C>T (0.35), inhA p.Ile194Thr (0.21), ethA c.1152dupT (0.36), ethA c.1152dupT (0.36)
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 0.37
lineage2 East-Asian Beijing RD105 0.43
lineage1 Indo-Oceanic EAI RD239 0.18
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.43
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.18
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.45
lineage1.2.2.2 Indo-Oceanic NA RD239 0.17
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 0.15 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.32 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.41 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.35 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 0.21 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.84 isoniazid
pncA 2288782 p.Arg154Gly missense_variant 0.2 pyrazinamide
pncA 2288847 p.Gly132Ala missense_variant 0.24 pyrazinamide
pncA 2289162 p.Leu27Pro missense_variant 0.18 pyrazinamide
pncA 2289206 p.Asp12Glu missense_variant 0.43 pyrazinamide
ald 3087252 c.436_437dupGC frameshift_variant 0.14 cycloserine
embB 4247429 p.Met306Val missense_variant 0.23 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.23 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.25 ethambutol
ethA 4326321 c.1152dupT frameshift_variant 0.36 ethionamide, ethionamide
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 0.21
gyrB 6112 p.Met291Ile missense_variant 0.2
gyrA 7268 c.-34C>T upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7581 p.Asp94Cys missense_variant 0.25
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.2
gyrA 9143 c.1842T>C synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 0.46
rpoB 759746 c.-61C>T upstream_gene_variant 0.38
rpoC 762434 c.-936T>G upstream_gene_variant 0.43
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.17
rpoC 763886 c.517C>A synonymous_variant 0.16
rpoC 764840 p.Ile491Val missense_variant 0.13
rpoC 765060 p.Asn564Ser missense_variant 0.17
rpoC 766466 p.Glu1033Lys missense_variant 0.37
rpoC 766488 p.Pro1040Arg missense_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 0.44
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.45
embR 1417019 p.Cys110Tyr missense_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471869 n.24G>A non_coding_transcript_exon_variant 0.18
rrs 1473368 n.1523G>A non_coding_transcript_exon_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 0.43
rpsA 1834940 p.Asp467Asn missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101727 p.Arg439Leu missense_variant 0.15
ndh 2102240 p.Arg268His missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 0.19
Rv1979c 2222700 c.465C>T synonymous_variant 0.38
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.44
pncA 2289365 c.-125delC upstream_gene_variant 0.4
kasA 2518132 c.18C>T synonymous_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 0.37
folC 2747453 p.Arg49Gln missense_variant 0.22
Rv2752c 3064700 p.Ser498Pro missense_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087601 p.Gly261Val missense_variant 0.2
Rv3083 3448714 p.Asp71His missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.19
fprA 3475159 p.Asn385Asp missense_variant 0.24
whiB7 3568428 c.252A>C synonymous_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 0.43
alr 3841473 c.-53G>A upstream_gene_variant 0.42
clpC1 4040517 p.Val63Ala missense_variant 0.16
clpC1 4040719 c.-15A>G upstream_gene_variant 0.19
embC 4240671 p.Thr270Ile missense_variant 0.18
embC 4241022 p.Ala387Val missense_variant 0.14
embC 4241042 p.Asn394Asp missense_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 0.39
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.5
embA 4245969 p.Pro913Ser missense_variant 0.19
embB 4247028 p.Leu172Arg missense_variant 0.2
embB 4247646 p.Glu378Ala missense_variant 0.2
aftB 4267492 p.Ala449Thr missense_variant 0.36
aftB 4267647 p.Asp397Gly missense_variant 0.43
ubiA 4269387 p.Glu149Asp missense_variant 0.15
aftB 4269606 c.-770T>C upstream_gene_variant 0.21
ethA 4326148 c.1326G>T synonymous_variant 0.16
ethA 4326439 p.Asn345Lys missense_variant 0.19
ethA 4326676 p.Ser266Arg missense_variant 0.24
whiB6 4338203 p.Arg107Cys missense_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.18
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407620 p.Tyr195His missense_variant 0.18
gid 4407790 p.Ala138Glu missense_variant 0.2
gid 4407848 p.Ala119Thr missense_variant 0.18
gid 4407873 c.330G>T synonymous_variant 0.2
gid 4407927 p.Glu92Asp missense_variant 0.39
gid 4407967 p.Leu79Trp missense_variant 0.4