TB-Profiler result

Run: ERR4596942
Summary

Run ID: ERR4596942

Sample name:

Date: 01-04-2023 06:30:40

Number of reads: 4316980

Percentage reads mapped: 99.51

Strain: lineage4;lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 0.95
lineage4 Euro-American LAM;T;S;X;H None 0.06
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.97
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.94
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 0.98 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
fgd1 491742 c.960T>C synonymous_variant 0.92
mshA 576108 p.Ala254Gly missense_variant 0.16
rpoB 759746 c.-61C>T upstream_gene_variant 0.92
rpoC 762434 c.-936T>G upstream_gene_variant 0.95
rpoC 763031 c.-339T>C upstream_gene_variant 0.87
rpoC 764666 p.Gly433Cys missense_variant 0.42
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.96
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304866 p.Gly646Arg missense_variant 0.95
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474024 n.367G>A non_coding_transcript_exon_variant 0.88
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.96
PPE35 2167926 p.Leu896Ser missense_variant 0.88
PPE35 2170461 p.Gly51Glu missense_variant 0.92
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.92
pncA 2289365 c.-125delC upstream_gene_variant 0.97
pncA 2289396 c.-155T>G upstream_gene_variant 0.97
ahpC 2726105 c.-88G>A upstream_gene_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
panD 4044443 c.-162G>C upstream_gene_variant 0.97
embC 4241562 p.Arg567His missense_variant 0.94
embC 4242075 p.Arg738Gln missense_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.9