TB-Profiler result

Run: ERR4814330
Summary

Run ID: ERR4814330

Sample name:

Date: 01-04-2023 13:13:53

Number of reads: 829910

Percentage reads mapped: 98.89

Strain: lineage4.6.2.2

Drug-resistance: Other

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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 1.0
lineage4.6 Euro-American T;LAM None 0.99
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 0.99
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
ethA 4326881 c.592delG frameshift_variant 0.13 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 5052 c.-188A>G upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8894 c.1593C>G synonymous_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620365 p.Asn159Asp missense_variant 0.13
rpoC 762797 c.-573C>T upstream_gene_variant 0.14
rpoC 766861 c.3492G>T synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776104 p.Ile793Leu missense_variant 0.18
mmpL5 777204 p.Pro426Leu missense_variant 0.17
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416498 p.Ser284Ala missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473953 n.296T>G non_coding_transcript_exon_variant 0.33
inhA 1674403 p.Glu68Lys missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918070 p.Thr44Asn missense_variant 0.4
ndh 2102302 c.741G>T synonymous_variant 0.25
PPE35 2169999 p.Ala205Gly missense_variant 0.29
PPE35 2170004 p.Ile203Asn missense_variant 0.25
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714620 p.Val238Asp missense_variant 0.2
folC 2746503 p.Leu366Met missense_variant 0.13
pepQ 2860125 p.Glu98Asp missense_variant 0.15
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612627 p.Ala164Thr missense_variant 0.25
rpoA 3878542 c.-35T>C upstream_gene_variant 0.14
clpC1 4039399 p.Glu436* stop_gained 0.12
embC 4241540 p.Thr560Ala missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0