TB-Profiler result

Run: ERR4407448
Summary

Run ID: ERR4407448

Sample name:

Date: 01-04-2023 05:44:29

Number of reads: 364570

Percentage reads mapped: 80.19

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 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
tlyA 1918517 c.582delC frameshift_variant 0.15 capreomycin
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 5269 c.31_33delGAA conservative_inframe_deletion 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7956 p.Val219Ile missense_variant 0.11
gyrA 8218 p.Ser306Phe missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620460 c.570T>C synonymous_variant 0.12
rpoB 759615 c.-192A>C upstream_gene_variant 0.29
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 762749 c.-621C>T upstream_gene_variant 0.15
rpoC 764479 p.Glu370Asp missense_variant 0.17
rpoC 764681 p.Leu438Met missense_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406362 c.978delA frameshift_variant 0.13
Rv1258c 1406860 p.Gly161Cys missense_variant 0.17
embR 1416730 c.618G>A synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102440 c.603C>T synonymous_variant 0.15
katG 2154221 p.Leu631Met missense_variant 0.1
PPE35 2169066 p.Ala516Glu missense_variant 0.11
PPE35 2169287 c.1326T>C synonymous_variant 0.18
PPE35 2169738 p.Thr292Leu missense_variant 0.13
PPE35 2169740 c.873C>T synonymous_variant 0.13
PPE35 2170030 p.Met195Leu missense_variant 0.14
PPE35 2170751 c.-139T>C upstream_gene_variant 0.1
Rv1979c 2222683 p.Trp161* stop_gained 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519140 c.1026G>C synonymous_variant 0.13
kasA 2519143 c.1029G>C synonymous_variant 0.12
folC 2746564 c.1035A>T synonymous_variant 0.12
folC 2746568 c.1030_1031insT frameshift_variant 0.12
Rv2752c 3064887 c.1305A>G synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339213 c.96G>A synonymous_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568780 c.-101A>G upstream_gene_variant 0.11
whiB7 3568782 c.-106_-104delACA upstream_gene_variant 0.11
whiB7 3568788 c.-109G>T upstream_gene_variant 0.1
whiB7 3568789 c.-110A>C upstream_gene_variant 0.1
Rv3236c 3612583 p.Trp178* stop_gained 0.17
fbiB 3642545 c.1011C>G synonymous_variant 0.22
ddn 3986974 p.Ile44Thr missense_variant 0.12
clpC1 4038802 p.Tyr635His missense_variant 0.14
embC 4239727 c.-136A>G upstream_gene_variant 0.11
embC 4239878 c.20delC frameshift_variant 0.12
embC 4241414 p.Arg518Ser missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245628 p.Pro799His missense_variant 0.1
embB 4248539 p.Phe676Leu missense_variant 0.11
ethR 4326583 c.-966G>A upstream_gene_variant 0.15
ethR 4327630 p.Ala28Thr missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0