TB-Profiler result

Run: ERR234613
Summary

Run ID: ERR234613

Sample name:

Date: 31-03-2023 18:07:25

Number of reads: 2747343

Percentage reads mapped: 99.65

Strain: lineage4.3.3;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 0.24
lineage4 Euro-American LAM;T;S;X;H None 0.76
lineage4.3 Euro-American (LAM) mainly-LAM None 0.76
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.27
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.24
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.72
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 0.24 rifampicin
rpoB 762089 p.Glu761Asp missense_variant 0.18 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.27 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.34 isoniazid
pncA 2289040 p.Trp68Arg missense_variant 0.29 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 0.29 kanamycin
embB 4247574 p.Asp354Ala missense_variant 0.25 ethambutol
ethA 4327480 c.-7T>C upstream_gene_variant 0.35 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.8
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.27
fgd1 491742 c.960T>C synonymous_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 0.38
rpoC 764995 c.1626C>G synonymous_variant 0.67
rpoC 766645 p.Glu1092Asp missense_variant 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.3
mmpL5 776182 p.Asp767Asn missense_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.64
Rv1258c 1406760 c.580_581insC frameshift_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674305 p.Gln35Arg missense_variant 0.77
rpsA 1834177 c.636A>C synonymous_variant 0.33
rpsA 1834836 p.Met432Thr missense_variant 0.78
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.27
katG 2156196 c.-85C>T upstream_gene_variant 0.79
PPE35 2167926 p.Leu896Ser missense_variant 0.21
PPE35 2169317 c.1296C>T synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.77
kasA 2519176 c.1062G>A synonymous_variant 0.71
folC 2746340 p.Ala420Val missense_variant 0.79
thyA 3073868 p.Thr202Ala missense_variant 0.65
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16
clpC1 4038287 c.2418C>T synonymous_variant 0.8
clpC1 4038857 c.1848C>A synonymous_variant 0.25
clpC1 4038968 c.1737G>A synonymous_variant 0.79
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.24
aftB 4267647 p.Asp397Gly missense_variant 0.29
whiB6 4338563 c.-42G>T upstream_gene_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.29
gid 4407927 p.Glu92Asp missense_variant 0.16
gid 4408156 p.Leu16Arg missense_variant 0.83