TB-Profiler result

Run: ERR1679640

Summary

Run ID: ERR1679640

Sample name:

Date: 31-03-2023 14:55:15

Number of reads: 385345

Percentage reads mapped: 99.82

Strain: lineage4.6.2.2

Drug-resistance: Sensitive


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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 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 1.0
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
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 7920 p.Asn207Tyr missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.18
rpoB 761705 c.1899C>T synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304030 p.Pro367His missense_variant 0.25
Rv1258c 1407264 p.Ser26Leu missense_variant 0.11
atpE 1460958 c.-87T>A upstream_gene_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472880 n.1035G>T non_coding_transcript_exon_variant 0.11
rrl 1475981 n.2324G>T non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154327 c.1785A>T synonymous_variant 0.11
katG 2155389 c.723C>G synonymous_variant 1.0
PPE35 2168029 p.Pro862Thr missense_variant 0.18
PPE35 2170082 c.531T>G synonymous_variant 0.18
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2222736 c.429C>T synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289221 c.21C>A synonymous_variant 0.2
pncA 2289416 c.-175T>A upstream_gene_variant 0.13
kasA 2518147 c.33C>T synonymous_variant 0.18
thyX 3067474 p.Pro158Ala missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
alr 3841581 c.-161T>C upstream_gene_variant 0.12
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243939 p.Trp236* stop_gained 0.12
embB 4246718 p.Ala69Thr missense_variant 0.18
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