TB-Profiler result

Run: ERR10748234
Summary

Run ID: ERR10748234

Sample name:

Date: 31-03-2023 10:48:22

Number of reads: 689304

Percentage reads mapped: 99.76

Strain: lineage4.1.1.2;lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.27
lineage4 Euro-American LAM;T;S;X;H None 0.73
lineage4.1 Euro-American T;X;H None 0.72
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.31
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.36
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.77
lineage4.1.1.2 Euro-American (X-type) X1 None 0.7
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 761155 p.Ser450Leu missense_variant 0.39 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.3 isoniazid
pncA 2288930 p.Ser104Arg missense_variant 0.32 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.33 ethambutol
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.34
ccsA 620625 p.Ile245Met missense_variant 0.31
rpoC 763031 c.-339T>C upstream_gene_variant 0.35
rpoC 765150 p.Gly594Glu missense_variant 0.57
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.41
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.27
katG 2155296 c.816C>T synonymous_variant 0.81
PPE35 2167926 p.Leu896Ser missense_variant 0.31
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449787 c.1284C>T synonymous_variant 0.76
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.26
alr 3840597 p.Met275Thr missense_variant 0.32
clpC1 4039676 c.1029G>A synonymous_variant 0.35
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.83
embA 4243460 c.228C>T synonymous_variant 0.24
embA 4243833 p.Ala201Thr missense_variant 0.71
embB 4246567 c.54G>T synonymous_variant 0.25
embB 4246930 p.Gln139His missense_variant 0.72
embB 4249408 c.2895G>A synonymous_variant 0.58
aftB 4267647 p.Asp397Gly missense_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.32
gid 4407927 p.Glu92Asp missense_variant 0.11