TB-Profiler result

Run: SRR25827744
Summary

Run ID: SRR25827744

Sample name:

Date: 02-02-2024 18:05:17

Number of reads: 9830290

Percentage reads mapped: 98.83

Strain: lineage2.2.1;lineage1.1.3.1

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (0.48), rpoC p.Ile491Thr (0.35)
Isoniazid R fabG1 c.-17G>T (0.40), katG p.Ser315Thr (0.40)
Ethambutol R embA c.-16C>T (0.42)
Pyrazinamide R pncA p.Ile5Ser (0.42)
Streptomycin R rpsL p.Lys43Arg (0.40)
Fluoroquinolones R gyrA p.Asp94Gly (0.36)
Moxifloxacin R gyrA p.Asp94Gly (0.36)
Ofloxacin R gyrA p.Asp94Gly (0.36)
Levofloxacin R gyrA p.Asp94Gly (0.36)
Ciprofloxacin R gyrA p.Asp94Gly (0.36)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (0.39)
Cycloserine
Ethionamide R fabG1 c.-17G>T (0.40), ethA c.1203delT (0.38)
Clofazimine
Para-aminosalicylic_acid R thyA p.Thr22Ala (0.42)
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 0.41
lineage1 Indo-Oceanic EAI RD239 0.56
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.58
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.42
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.55
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.4
lineage1.1.3.1 Indo-Oceanic NA RD239 0.56
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 7582 p.Asp94Gly missense_variant 0.36 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.48 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.35 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.4 streptomycin
fabG1 1673423 c.-17G>T upstream_gene_variant 0.4 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.4 isoniazid
pncA 2289228 p.Ile5Ser missense_variant 0.42 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.39 kanamycin
thyA 3074408 p.Thr22Ala missense_variant 0.42 para-aminosalicylic_acid
embA 4243217 c.-16C>T upstream_gene_variant 0.42 ethambutol
ethA 4326270 c.1203delT frameshift_variant 0.38 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 6112 p.Met291Ile missense_variant 0.59
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.55
gyrA 9143 c.1842T>C synonymous_variant 0.53
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.53
fgd1 491742 c.960T>C synonymous_variant 0.98
mshA 575907 p.Ala187Val missense_variant 0.42
ccsA 620625 p.Ile245Met missense_variant 0.43
rpoC 763031 c.-339T>C upstream_gene_variant 0.97
rpoC 763884 p.Ala172Val missense_variant 0.54
rpoC 763886 c.517C>A synonymous_variant 0.54
rpoC 765171 p.Pro601Leu missense_variant 0.63
rpoC 765230 p.Ala621Thr missense_variant 0.6
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 0.42
mmpS5 779526 c.-621G>A upstream_gene_variant 0.59
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 0.43
embR 1417019 p.Cys110Tyr missense_variant 0.48
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.42
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918254 c.315C>T synonymous_variant 0.59
ndh 2102380 c.663G>T synonymous_variant 0.54
katG 2154724 p.Arg463Leu missense_variant 0.98
katG 2155416 c.696G>A synonymous_variant 0.54
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.56
Rv1979c 2222308 p.Asp286Gly missense_variant 0.57
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.56
ahpC 2726051 c.-142G>A upstream_gene_variant 0.57
Rv2752c 3064632 c.1560C>T synonymous_variant 0.54
thyX 3067949 c.-4C>T upstream_gene_variant 0.48
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.56
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.58
fprA 3475159 p.Asn385Asp missense_variant 0.55
Rv3236c 3612813 p.Thr102Ala missense_variant 0.4
alr 3841253 c.168C>T synonymous_variant 0.45
rpoA 3878637 c.-130G>C upstream_gene_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 0.54
embC 4240671 p.Thr270Ile missense_variant 0.57
embC 4241022 p.Ala387Val missense_variant 0.43
embC 4241042 p.Asn394Asp missense_variant 0.58
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.43
embA 4243848 p.Val206Met missense_variant 0.53
embA 4245969 p.Pro913Ser missense_variant 0.58
embB 4247646 p.Glu378Ala missense_variant 0.54
embB 4247847 p.Gln445Arg missense_variant 0.32
aftB 4267647 p.Asp397Gly missense_variant 0.33
ubiA 4269387 p.Glu149Asp missense_variant 0.61
aftB 4269606 c.-770T>C upstream_gene_variant 0.55
ethA 4327546 c.-73T>A upstream_gene_variant 0.51
whiB6 4338292 p.Ala77Val missense_variant 0.43
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407620 p.Tyr195His missense_variant 0.4
gid 4407780 c.423G>A synonymous_variant 0.54
gid 4407873 c.330G>T synonymous_variant 0.57
gid 4407927 p.Glu92Asp missense_variant 0.38