TB-Profiler result

Run: ERR4407470
Summary

Run ID: ERR4407470

Sample name:

Date: 01-04-2023 05:45:29

Number of reads: 244743

Percentage reads mapped: 99.58

Strain: lineage4.6.2.2

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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 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
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, 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 5749 c.510G>A synonymous_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7762 p.Pro154Arg missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.29
ccsA 620748 c.858T>G synonymous_variant 0.33
rpoB 763037 c.3232delA frameshift_variant 0.12
rpoC 766361 p.Val998Met missense_variant 0.18
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 1304863 p.Ser645Gly missense_variant 0.22
Rv1258c 1406994 p.Phe116Tyr missense_variant 0.11
Rv1258c 1407006 p.Leu112Arg missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472222 n.377G>T non_coding_transcript_exon_variant 0.12
rrs 1473022 n.1177G>T non_coding_transcript_exon_variant 0.17
rrs 1473076 n.1231A>G non_coding_transcript_exon_variant 0.13
rrl 1473744 n.87T>C non_coding_transcript_exon_variant 0.25
rrl 1473941 n.284T>C non_coding_transcript_exon_variant 1.0
rrl 1473968 n.314_315dupGG non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715432 c.-100C>T upstream_gene_variant 0.1
eis 2715436 c.-104G>A upstream_gene_variant 0.11
eis 2715440 c.-108A>C upstream_gene_variant 0.11
eis 2715445 c.-113C>T upstream_gene_variant 0.11
eis 2715447 c.-115T>A upstream_gene_variant 0.11
eis 2715450 c.-118T>C upstream_gene_variant 0.11
eis 2715451 c.-119C>A upstream_gene_variant 0.11
eis 2715454 c.-122T>G upstream_gene_variant 0.11
eis 2715455 c.-123G>A upstream_gene_variant 0.11
eis 2715458 c.-126T>A upstream_gene_variant 0.11
eis 2715460 c.-128A>G upstream_gene_variant 0.11
eis 2715465 c.-133G>T upstream_gene_variant 0.12
eis 2715469 c.-137T>C upstream_gene_variant 0.12
eis 2715473 c.-141A>G upstream_gene_variant 0.12
ahpC 2726338 p.Val49Gly missense_variant 0.25
ahpC 2726626 p.Gln145Arg missense_variant 0.18
thyX 3067246 c.699delC frameshift_variant 0.5
thyX 3067474 p.Pro158Ala missense_variant 1.0
ald 3086792 c.-28G>T upstream_gene_variant 0.12
fbiD 3339273 c.156T>G synonymous_variant 0.22
fbiD 3339441 c.324C>A synonymous_variant 0.17
Rv3083 3448567 p.His22Asp missense_variant 1.0
Rv3083 3448965 c.462C>A synonymous_variant 0.29
Rv3083 3449589 c.1086C>T synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4039594 p.Arg371Gly missense_variant 0.12
panD 4043978 p.Gln102Lys missense_variant 0.11
embC 4239732 c.-131T>C upstream_gene_variant 0.11
embC 4240648 c.786C>T synonymous_variant 0.22
embC 4240766 c.904C>A synonymous_variant 0.15
embC 4240828 c.968delC frameshift_variant 0.11
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