TB-Profiler result

Run: ERR279534
Summary

Run ID: ERR279534

Sample name:

Date: 31-03-2023 23:40:00

Number of reads: 3132743

Percentage reads mapped: 99.51

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
ethR 4327876 p.Phe110Leu missense_variant 1.0 ethionamide
ethA 4274706 c.-26093_*51297del transcript_ablation 1.0 ethionamide
ethA 4303397 c.-25909_*22606del transcript_ablation 1.0 ethionamide
ethA 4309260 c.-56203_*16743del transcript_ablation 1.0 ethionamide
ethA 4319621 c.-63058_*6382del transcript_ablation 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8512 p.Val404Gly missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
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
rplC 800889 c.81C>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168303 c.2310G>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840263 c.1158C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.26
embC 4242422 p.Trp854Gly missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
aftB 4267091 c.1746C>A synonymous_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
rpsA 1779273 c.-54268_*43456del transcript_ablation 1.0
tlyA 1878825 c.-39114_*40809del transcript_ablation 1.0
tlyA 1879407 c.-38532_*29880del transcript_ablation 1.0
tlyA 1884651 c.-33288_*516del transcript_ablation 1.0
tlyA 1889528 c.-28411_*50337del transcript_ablation 1.0
tlyA 1889551 c.-28388_*9028del transcript_ablation 1.0
tlyA 1890075 c.-27864_*63351del transcript_ablation 1.0
eis 2651269 c.-32922_*62854del transcript_ablation 1.0
pepQ 2804472 c.-42738_*54827del transcript_ablation 1.0
ribD 2961559 c.-25279_*10615del transcript_ablation 1.0
ribD 2961752 c.-25086_*54101del transcript_ablation 1.0
fbiD 3287535 c.-51582_*16949del transcript_ablation 1.0
fbiD 3294560 c.-44557_*14210del transcript_ablation 1.0
fprA 3472159 c.-1847_*52325del transcript_ablation 1.0
whiB7 3528972 c.-48071_*39428del transcript_ablation 1.0
Rv3236c 3581406 c.-41013_*30552del transcript_ablation 1.0
Rv3236c 3585137 c.624_*26821del frameshift_variant&stop_lost&splice_region_variant 1.0
Rv3236c 3611871 c.-19849_*87del transcript_ablation 1.0
alr 3766799 c.-8277_*73394del transcript_ablation 1.0
alr 3838384 c.-2819_*1809del transcript_ablation 1.0
clpC1 4031669 c.-67133_*6488del transcript_ablation 1.0
clpC1 4037102 c.-7389_*1055del transcript_ablation 1.0