TB-Profiler result

Run: SRR6964676

Summary

Run ID: SRR6964676

Sample name:

Date: 04-04-2023 18:21:27

Number of reads: 3716542

Percentage reads mapped: 99.71

Strain: lineage4.9;lineage3

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
lineage3 East-African-Indian CAS RD750 0.15
lineage4 Euro-American LAM;T;S;X;H None 0.84
lineage4.9 Euro-American (H37Rv-like) T1 None 0.85
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 0.91 rifampicin
inhA 1674481 p.Ser94Ala missense_variant 0.83 isoniazid, 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
gyrB 5078 c.-162_-161insG upstream_gene_variant 0.43
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9163 p.Pro621Leu missense_variant 0.83
fgd1 491742 c.960T>C synonymous_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 0.1
rpoC 762434 c.-936T>G upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834856 p.Glu439Lys missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.19
PPE35 2167926 p.Leu896Ser missense_variant 0.2
PPE35 2169844 p.Ile257Val missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.2
PPE35 2170053 p.Thr187Ser missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288950 p.Ala98Ser missense_variant 0.15
pncA 2289047 c.195C>T synonymous_variant 0.2
pncA 2289365 c.-125delC upstream_gene_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.14
ddn 3986818 c.-26G>T upstream_gene_variant 0.16
embC 4242075 p.Arg738Gln missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.19
gid 4408023 p.Glu60Asp missense_variant 0.14