TB-Profiler result

Run: ERR4800221
Summary

Run ID: ERR4800221

Sample name:

Date: 20-10-2023 04:15:18

Number of reads: 2128794

Percentage reads mapped: 99.39

Strain: lineage2.2.1;lineage1.1.2

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (0.54)
Ethambutol R embB p.Met306Val (0.48), embB p.Gln853Pro (0.29)
Pyrazinamide R pncA c.391dupG (0.45), pncA c.391dupG (0.45)
Streptomycin R rpsL p.Lys43Arg (0.43)
Fluoroquinolones R gyrA p.Asp94Gly (0.45)
Moxifloxacin R gyrA p.Asp94Gly (0.45)
Ofloxacin R gyrA p.Asp94Gly (0.45)
Levofloxacin R gyrA p.Asp94Gly (0.45)
Ciprofloxacin R gyrA p.Asp94Gly (0.45)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.1047dupT (0.38), ethA c.1047dupT (0.38)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.45)
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 0.46
lineage1 Indo-Oceanic EAI RD239 0.58
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.55
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.45
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.53
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.4
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 0.45 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpsL 781687 p.Lys43Arg missense_variant 0.43 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.54 isoniazid
pncA 2288850 c.391dupG frameshift_variant 0.45 pyrazinamide, pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.45 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.48 ethambutol
embB 4249071 p.Gln853Pro missense_variant 0.29 ethambutol
ethA 4326426 c.1047dupT frameshift_variant 0.38 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 0.51
gyrB 6124 c.885C>T synonymous_variant 0.55
gyrA 7283 c.-19G>T upstream_gene_variant 0.53
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.6
gyrA 9062 c.1761C>G synonymous_variant 0.64
gyrA 9143 c.1842T>C synonymous_variant 0.58
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.49
ccsA 620625 p.Ile245Met missense_variant 0.48
rpoB 760490 c.684C>T synonymous_variant 0.48
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763884 p.Ala172Val missense_variant 0.42
rpoC 763886 c.517C>A synonymous_variant 0.42
rpoC 764666 p.Gly433Ser missense_variant 0.54
rpoC 765171 p.Pro601Leu missense_variant 0.55
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 0.34
mmpL5 776395 p.Phe696Leu missense_variant 0.57
mmpS5 779615 c.-710C>G upstream_gene_variant 0.53
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 0.71
atpE 1460890 c.-155G>T upstream_gene_variant 0.56
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102791 c.252A>C synonymous_variant 0.46
katG 2153967 c.2145C>T synonymous_variant 0.58
katG 2154724 p.Arg463Leu missense_variant 0.98
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.58
PPE35 2170785 c.-173T>C upstream_gene_variant 0.6
Rv1979c 2222308 p.Asp286Gly missense_variant 0.6
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.44
eis 2715016 p.Arg106His missense_variant 0.64
ahpC 2726051 c.-142G>A upstream_gene_variant 0.44
pepQ 2860365 c.54G>T synonymous_variant 0.35
Rv2752c 3064632 c.1560C>T synonymous_variant 0.49
Rv2752c 3065419 p.Arg258Leu missense_variant 0.7
thyA 3074069 p.Val135Phe missense_variant 0.42
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.53
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.53
fprA 3475159 p.Asn385Asp missense_variant 0.69
Rv3236c 3612813 p.Thr102Ala missense_variant 0.43
rpoA 3878575 c.-68C>A upstream_gene_variant 0.56
clpC1 4040517 p.Val63Ala missense_variant 0.45
embC 4240671 p.Thr270Ile missense_variant 0.43
embC 4241042 p.Asn394Asp missense_variant 0.65
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 0.44
embA 4243460 c.228C>T synonymous_variant 0.46
embA 4243848 p.Val206Met missense_variant 0.53
embA 4245969 p.Pro913Ser missense_variant 0.52
embB 4247646 p.Glu378Ala missense_variant 0.54
embB 4249757 p.Thr1082Ala missense_variant 0.38
aftB 4267647 p.Asp397Gly missense_variant 0.57
ubiA 4269387 p.Glu149Asp missense_variant 0.56
aftB 4269606 c.-770T>C upstream_gene_variant 0.47
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.58
gid 4407588 c.615A>G synonymous_variant 0.98
gid 4407873 c.330G>T synonymous_variant 0.58
gid 4407927 p.Glu92Asp missense_variant 0.49