TB-Profiler result

Run: ERR2229231
Summary

Run ID: ERR2229231

Sample name:

Date: 31-03-2023 16:50:41

Number of reads: 1105566

Percentage reads mapped: 99.1

Strain: lineage4.8

Drug-resistance: RR-TB

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rpoB 761107 p.Met434Thr missense_variant 0.14 rifampicin
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
mshA 575344 c.-4A>T upstream_gene_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.19
rpoB 760525 p.Glu240Val missense_variant 0.12
rpoC 762704 c.-666G>C upstream_gene_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775992 p.Glu830Val missense_variant 0.13
mmpL5 777553 p.Val310Met missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475222 n.1565G>T non_coding_transcript_exon_variant 0.2
rrl 1475455 n.1798C>T non_coding_transcript_exon_variant 0.25
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.16
fabG1 1673361 c.-79C>G upstream_gene_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
inhA 1674938 p.Leu246Pro missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155193 p.Gly307* stop_gained 0.15
katG 2155878 c.234G>T synonymous_variant 0.18
PPE35 2167733 c.2880G>T synonymous_variant 0.12
PPE35 2167736 c.2877G>T synonymous_variant 0.12
PPE35 2167955 c.2658A>C synonymous_variant 0.11
PPE35 2167965 p.Ala883Gly missense_variant 0.22
PPE35 2167967 c.2646A>C synonymous_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.19
PPE35 2169272 c.1341C>G synonymous_variant 0.17
PPE35 2169278 c.1335T>C synonymous_variant 0.17
PPE35 2169281 c.1332T>G synonymous_variant 0.15
PPE35 2169725 c.888T>C synonymous_variant 0.17
PPE35 2169910 p.Asn235Tyr missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.22
PPE35 2170053 p.Thr187Ser missense_variant 0.24
PPE35 2170308 p.Leu102Pro missense_variant 0.12
PPE35 2170534 p.Ala27Thr missense_variant 0.12
Rv1979c 2222535 c.630C>A synonymous_variant 0.14
Rv1979c 2222940 p.Asn75Lys missense_variant 0.12
Rv1979c 2223043 p.Gly41Val missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519128 c.1014G>C synonymous_variant 0.13
kasA 2519131 c.1017G>C synonymous_variant 0.13
folC 2746441 c.1158C>T synonymous_variant 0.15
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612348 p.Asp257Tyr missense_variant 0.2
Rv3236c 3612441 p.Thr226Ser missense_variant 0.13
clpC1 4039645 p.His354Asp missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244686 p.Ile485Asn missense_variant 0.18
embA 4244834 c.1602G>C synonymous_variant 0.29
embB 4246709 p.Ser66Gly missense_variant 0.17
embB 4248000 p.Asp496Val missense_variant 0.12
aftB 4267254 p.His528Leu missense_variant 0.18
ethA 4326456 p.Thr340Ala missense_variant 0.12
ethA 4327163 p.Val104Ala missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408214 c.-12G>T upstream_gene_variant 0.11
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0