TB-Profiler result

Run: ERR4553510
Summary

Run ID: ERR4553510

Sample name:

Date: 01-04-2023 06:12:01

Number of reads: 1493398

Percentage reads mapped: 99.67

Strain: lineage4

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
lineage4 Euro-American LAM;T;S;X;H None 0.75
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.18
lineage1.1.3.3 Indo-Oceanic NA RD239 0.19
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 0.68 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.68 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289186 p.Leu19Arg missense_variant 0.66 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.5 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
gyrB 6061 p.Ser274Arg missense_variant 0.75
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.34
mshA 576108 p.Ala254Gly missense_variant 0.28
rpoB 759628 c.-179C>T upstream_gene_variant 0.7
rpoC 763031 c.-339T>C upstream_gene_variant 0.25
rpoC 765230 p.Ala621Thr missense_variant 0.12
rpoC 767123 p.Val1252Leu missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.3
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407255 p.Ala29Glu missense_variant 0.67
embR 1416468 p.Asp294Asn missense_variant 0.24
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473293 n.1448G>C non_coding_transcript_exon_variant 0.52
rrl 1475049 n.1392C>T non_coding_transcript_exon_variant 0.18
inhA 1673393 c.-809G>A upstream_gene_variant 0.73
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.33
katG 2156146 c.-35A>G upstream_gene_variant 0.21
PPE35 2167926 p.Leu896Ser missense_variant 0.14
PPE35 2169779 c.834A>C synonymous_variant 0.67
Rv1979c 2222308 p.Asp286Gly missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288772 p.Val157Gly missense_variant 0.29
pncA 2289256 c.-15A>C upstream_gene_variant 0.57
kasA 2518132 c.18C>T synonymous_variant 0.14
folC 2746365 c.1234C>T synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.26
fprA 3474299 p.Asp98Gly missense_variant 0.67
Rv3236c 3613279 c.-163C>A upstream_gene_variant 0.13
panD 4043957 p.Asp109Asn missense_variant 0.72
embC 4240671 p.Thr270Ile missense_variant 0.27
embC 4241736 p.Val625Ala missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.2
embB 4247351 p.Asp280Tyr missense_variant 0.2
embB 4248516 p.Val668Ala missense_variant 0.11
aftB 4266975 p.Pro621Arg missense_variant 0.19
ethA 4328317 c.-844C>T upstream_gene_variant 0.69
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.2
gid 4407780 c.423G>A synonymous_variant 0.11