TB-Profiler result

Run: ERR3077998

Summary

Run ID: ERR3077998

Sample name:

Date: 01-04-2023 00:15:52

Number of reads: 7304480

Percentage reads mapped: 99.46

Strain: lineage4.2.2.2;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 0.83
lineage4 Euro-American LAM;T;S;X;H None 0.15
lineage4.2 Euro-American H;T;LAM None 0.16
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.82
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.14
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.84
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.14
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 761100 p.Gln432Glu missense_variant 0.13 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.86 rifampicin
rpsL 781822 p.Lys88Met missense_variant 0.18 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288859 p.Val128Gly missense_variant 0.82 pyrazinamide
embB 4247429 p.Met306Leu missense_variant 0.14 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.84 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.87 ethambutol
ethA 4326208 c.1265_1266insT frameshift_variant 0.85 ethionamide
gid 4407731 c.471delG frameshift_variant 0.83 streptomycin
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 8688 p.Ala463Ser missense_variant 0.23
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.88
mshA 576077 c.730C>T synonymous_variant 0.11
rpoB 759746 c.-61C>T upstream_gene_variant 0.84
rpoB 761248 p.Glu481Ala missense_variant 0.13
rpoB 761407 p.Val534Ala missense_variant 0.89
rpoC 762434 c.-936T>G upstream_gene_variant 0.84
rpoC 763031 c.-339T>C upstream_gene_variant 0.82
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.86
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.88
PPE35 2167926 p.Leu896Ser missense_variant 0.87
PPE35 2170461 p.Gly51Glu missense_variant 0.88
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288911 p.Glu111* stop_gained 0.15
pncA 2289047 c.195C>T synonymous_variant 0.84
pncA 2289365 c.-125delC upstream_gene_variant 0.84
ahpC 2726105 c.-88G>A upstream_gene_variant 0.86
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.16
ald 3086742 c.-78A>C upstream_gene_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240172 p.Val104Met missense_variant 0.88
embC 4241562 p.Arg567His missense_variant 0.84
embC 4242075 p.Arg738Gln missense_variant 0.86
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243323 p.Val31Ile missense_variant 0.84
ethR 4328051 p.Ala168Val missense_variant 0.8
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.86