TB-Profiler result

Run: SRR25827629

Summary

Run ID: SRR25827629

Sample name:

Date: 02-02-2024 12:13:18

Number of reads: 6742512

Percentage reads mapped: 99.02

Strain: lineage3;lineage2.2.1;lineage1.1.3.3

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 (0.97)
Isoniazid R katG p.Ser315Thr (0.99)
Ethambutol R embB p.Met306Val (0.59)
Pyrazinamide R pncA p.Thr177Pro (0.32), pncA c.390_391dupGG (0.34), pncA c.390_391dupGG (0.34)
Streptomycin R rpsL p.Lys43Arg (0.37)
Fluoroquinolones R gyrA p.Ala90Val (0.23), gyrA p.Asp94Gly (0.34)
Moxifloxacin R gyrA p.Ala90Val (0.23), gyrA p.Asp94Gly (0.34)
Ofloxacin R gyrA p.Ala90Val (0.23), gyrA p.Asp94Gly (0.34)
Levofloxacin R gyrA p.Ala90Val (0.23), gyrA p.Asp94Gly (0.34)
Ciprofloxacin R gyrA p.Ala90Val (0.23), gyrA p.Asp94Gly (0.34)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.110delA (0.24), ethA c.110delA (0.24)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.34)
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 0.3
lineage2 East-Asian Beijing RD105 0.33
lineage1 Indo-Oceanic EAI RD239 0.36
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.35
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.32
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.36
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.32
lineage1.1.3.3 Indo-Oceanic NA RD239 0.37
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 0.23 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.34 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.37 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2288713 p.Thr177Pro missense_variant 0.32 pyrazinamide
pncA 2288850 c.390_391dupGG frameshift_variant 0.34 pyrazinamide, pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.34 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.59 ethambutol
ethA 4327363 c.110delA frameshift_variant 0.24 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 6112 p.Met291Ile missense_variant 0.32
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.36
gyrA 9143 c.1842T>C synonymous_variant 0.34
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.98
mshA 575907 p.Ala187Val missense_variant 0.31
ccsA 620625 p.Ile245Met missense_variant 0.26
rpoB 759746 c.-61C>T upstream_gene_variant 0.28
rpoB 759940 p.Pro45Leu missense_variant 0.29
rpoC 762434 c.-936T>G upstream_gene_variant 0.32
rpoC 763031 c.-339T>C upstream_gene_variant 0.96
rpoC 763884 p.Ala172Val missense_variant 0.42
rpoC 763886 c.517C>A synonymous_variant 0.42
rpoC 764840 p.Ile491Val missense_variant 0.37
rpoC 765171 p.Pro601Leu missense_variant 0.38
rpoC 765230 p.Ala621Thr missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776006 c.2475C>T synonymous_variant 0.29
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 0.37
mmpL5 776826 p.Glu552Gly missense_variant 0.26
mmpS5 779615 c.-710C>G upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.29
embR 1417019 p.Cys110Tyr missense_variant 0.43
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.32
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103062 c.-20C>T upstream_gene_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 0.97
PPE35 2167926 p.Leu896Ser missense_variant 0.99
PPE35 2167983 p.Gly877Asp missense_variant 0.39
PPE35 2168124 p.Gly830Glu missense_variant 0.36
PPE35 2169630 p.Asn328Ser missense_variant 0.35
PPE35 2169757 p.Asn286Asp missense_variant 0.37
Rv1979c 2222308 p.Asp286Gly missense_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.27
kasA 2518132 c.18C>T synonymous_variant 0.34
kasA 2519100 p.Ala329Val missense_variant 0.34
ahpC 2726051 c.-142G>A upstream_gene_variant 0.3
ahpC 2726105 c.-88G>A upstream_gene_variant 0.33
folC 2747666 c.-68A>G upstream_gene_variant 0.37
Rv2752c 3064632 c.1560C>T synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.38
Rv3083 3449709 c.1206C>G synonymous_variant 0.38
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474358 p.Asp118His missense_variant 0.35
fprA 3474597 c.591C>A synonymous_variant 0.34
fprA 3475159 p.Asn385Asp missense_variant 0.36
whiB7 3568425 c.255T>G synonymous_variant 0.16
Rv3236c 3612813 p.Thr102Ala missense_variant 0.28
fbiB 3642877 p.Lys448Arg missense_variant 0.23
alr 3840493 c.928C>T synonymous_variant 0.35
alr 3841349 c.72C>A synonymous_variant 0.4
alr 3841362 p.Thr20Met missense_variant 0.35
clpC1 4040315 c.390G>A synonymous_variant 0.34
clpC1 4040517 p.Val63Ala missense_variant 0.35
embC 4240207 c.345G>A synonymous_variant 0.35
embC 4240671 p.Thr270Ile missense_variant 0.31
embC 4241022 p.Ala387Val missense_variant 0.33
embC 4241042 p.Asn394Asp missense_variant 0.34
embC 4242075 p.Arg738Gln missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.31
embA 4243848 p.Val206Met missense_variant 0.43
embA 4245969 p.Pro913Ser missense_variant 0.39
embB 4247028 p.Leu172Arg missense_variant 0.15
embB 4247646 p.Glu378Ala missense_variant 0.28
aftB 4267431 p.Ser469Leu missense_variant 0.32
aftB 4267647 p.Asp397Gly missense_variant 0.29
ubiA 4269387 p.Glu149Asp missense_variant 0.37
aftB 4269606 c.-770T>C upstream_gene_variant 0.41
whiB6 4338208 p.Pro105Gln missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.37
gid 4407588 c.615A>G synonymous_variant 0.97
gid 4407620 p.Tyr195His missense_variant 0.27
gid 4407766 p.Thr146Arg missense_variant 0.32
gid 4407780 c.423G>A synonymous_variant 0.32
gid 4407873 c.330G>T synonymous_variant 0.33
gid 4407927 p.Glu92Asp missense_variant 0.3
gid 4408060 p.His48Arg missense_variant 0.28