TB-Profiler result

Run: ERR2229041
Summary

Run ID: ERR2229041

Sample name:

Date: 31-03-2023 16:31:33

Number of reads: 571552

Percentage reads mapped: 99.29

Strain: lineage4.8

Drug-resistance: HR-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
katG 2155350 c.761_762insTCGTT frameshift_variant 0.18 isoniazid
pncA 2289150 p.Ile31Thr missense_variant 0.22 pyrazinamide
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 7962 p.Gly221Trp missense_variant 0.22
gyrA 9801 p.Asp834Tyr missense_variant 0.2
rpoB 762516 p.Gly904Ser missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776041 p.Ala814Ser missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304371 p.His481Asn missense_variant 0.33
Rv1258c 1407191 c.150G>T synonymous_variant 0.13
atpE 1461080 c.36C>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476254 n.2597C>A non_coding_transcript_exon_variant 0.22
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 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.45
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167814 c.2799C>T synonymous_variant 0.18
PPE35 2168047 p.Leu856Val missense_variant 0.12
PPE35 2168051 p.Val854Ile missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.19
PPE35 2169281 c.1332T>G synonymous_variant 0.2
PPE35 2169287 c.1326T>C synonymous_variant 0.21
PPE35 2169293 c.1320T>C synonymous_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.4
PPE35 2170053 p.Thr187Ser missense_variant 0.42
Rv1979c 2222032 p.Ala378Glu missense_variant 0.12
Rv1979c 2222559 c.601_605dupAGCGC frameshift_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.33
ahpC 2726134 c.-59C>T upstream_gene_variant 0.13
pepQ 2860162 p.Arg86Pro missense_variant 0.18
ribD 2987097 p.Thr87Ser missense_variant 0.25
ribD 2987323 p.Val162Gly missense_variant 0.5
Rv3236c 3613299 c.-183C>T upstream_gene_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242648 p.Leu929Arg missense_variant 0.4
embB 4246544 p.Thr11Pro missense_variant 0.43
embB 4249652 p.His1047Tyr missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0