TB-Profiler result

Run: ERR4820942
Summary

Run ID: ERR4820942

Sample name:

Date: 01-04-2023 16:58:12

Number of reads: 835996

Percentage reads mapped: 99.33

Strain: lineage1.1.2

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 1.0
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
rpoB 761101 p.Gln432Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288757 p.Gly162Asp missense_variant 1.0 pyrazinamide
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
ethA 4326439 c.1034delA frameshift_variant 1.0 ethionamide, ethionamide
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin
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 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9047 c.1746C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575782 c.435G>T synonymous_variant 1.0
mshA 576000 p.Asp218Ala missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.19
rpoB 760072 p.Pro89Leu missense_variant 0.15
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 764969 p.Ala534Pro missense_variant 0.11
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765973 c.2604C>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpL5 776923 p.Ala520Thr missense_variant 0.13
mmpL5 777179 c.1302G>A synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460983 c.-61delG upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102263 c.779delA frameshift_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169461 c.1152C>T synonymous_variant 0.13
PPE35 2170519 p.Asp32His missense_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290110 c.-869C>A upstream_gene_variant 0.25
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064859 p.Gly445Ser missense_variant 0.15
Rv2752c 3065643 c.549C>A synonymous_variant 0.12
Rv2752c 3065854 p.Ala113Glu missense_variant 0.12
Rv2752c 3065921 p.Pro91Thr missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448599 p.Ile32Met missense_variant 0.11
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448903 p.Asp134Asn missense_variant 0.33
fprA 3473882 c.-125A>G upstream_gene_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612921 p.Val66Phe missense_variant 0.13
fbiB 3642850 p.Val439Gly missense_variant 0.16
clpC1 4038197 c.2508A>G synonymous_variant 0.13
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240166 p.Lys102Glu missense_variant 0.11
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241828 p.Lys656Glu missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408224 c.-22T>A upstream_gene_variant 0.11