TB-Profiler result

Run: ERR4830357

Summary

Run ID: ERR4830357

Sample name:

Date: 20-10-2023 13:16:39

Number of reads: 3305465

Percentage reads mapped: 98.41

Strain: lineage2.2.1.1;lineage1.1

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 (0.86)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.90)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R folC p.Glu40Gly (0.89)
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 0.88
lineage1 Indo-Oceanic EAI RD239 0.06
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.13
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.85
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.9
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.9
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
rpsL 781687 p.Lys43Arg missense_variant 0.9 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.86 isoniazid
folC 2747480 p.Glu40Gly missense_variant 0.89 para-aminosalicylic_acid
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 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.9
ccsA 620625 p.Ile245Met missense_variant 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.92
mmpS5 779615 c.-710C>G upstream_gene_variant 0.92
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.88
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.97
rpsA 1834319 p.Val260Ile missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154264 c.1848G>A synonymous_variant 0.96
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.22
PPE35 2169122 c.1491C>G synonymous_variant 0.12
PPE35 2169125 p.Val496Ile missense_variant 0.13
PPE35 2169131 c.1482C>T synonymous_variant 0.13
PPE35 2169134 c.1479G>A synonymous_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 0.89
ahpC 2726051 c.-142G>A upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 0.2
Rv3083 3448714 p.Asp71His missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.14
fprA 3475159 p.Asn385Asp missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 0.95
rpoA 3878630 c.-124delC upstream_gene_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.93
embA 4245969 p.Pro913Ser missense_variant 0.13
embB 4248115 c.1602C>T synonymous_variant 0.89
aftB 4267647 p.Asp397Gly missense_variant 0.9
ubiA 4269387 p.Glu149Asp missense_variant 0.15
aftB 4269606 c.-770T>C upstream_gene_variant 0.1
whiB6 4338242 p.Gln94Glu missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.17
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.21
gid 4407927 p.Glu92Asp missense_variant 0.82