TB-Profiler result

Run: ERR1679655

Summary

Run ID: ERR1679655

Sample name:

Date: 31-03-2023 14:55:36

Number of reads: 432794

Percentage reads mapped: 99.67

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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.27
fgd1 491199 p.Met139Ile missense_variant 0.29
ccsA 620128 p.Gly80Trp missense_variant 0.4
rpoB 759620 c.-187A>C upstream_gene_variant 0.32
rpoB 761152 p.Leu449Gln missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776984 p.Phe499Leu missense_variant 0.17
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304475 c.1545G>C synonymous_variant 0.15
embR 1416951 p.Gln133Lys missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834901 p.Ala454Ser missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102761 c.282G>A synonymous_variant 0.12
katG 2155061 p.Trp351Arg missense_variant 0.13
katG 2155389 c.723C>G synonymous_variant 1.0
PPE35 2169881 p.Ser244Arg missense_variant 0.2
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289379 c.-138T>G upstream_gene_variant 0.12
pncA 2290146 c.-905G>T upstream_gene_variant 0.12
folC 2746850 p.Val250Glu missense_variant 0.15
folC 2747280 p.Arg107Cys missense_variant 0.18
Rv2752c 3064612 p.Ile527Thr missense_variant 0.12
Rv2752c 3064659 c.1532dupT frameshift_variant 0.12
Rv2752c 3064838 c.1354T>C synonymous_variant 0.2
thyX 3067460 c.486G>A synonymous_variant 0.22
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
fbiB 3642085 p.Gly184Ala missense_variant 0.4
rpoA 3878237 p.Glu91* stop_gained 0.11
clpC1 4039550 c.1155G>T synonymous_variant 0.13
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242655 c.-578A>G upstream_gene_variant 0.12
embA 4244005 p.Ile258Ser missense_variant 0.2
embA 4245535 p.Ser768Ile missense_variant 0.22
embB 4248231 p.Arg573Leu missense_variant 0.14
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4268887 c.-51C>T upstream_gene_variant 0.11
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