TB-Profiler result

Run: ERR2229217
Summary

Run ID: ERR2229217

Sample name:

Date: 31-03-2023 16:49:04

Number of reads: 177342

Percentage reads mapped: 99.55

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.09
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
embB 4247467 p.Asn318Lys missense_variant 0.25 ethambutol
ethA 4326424 c.1049dupG frameshift_variant 0.67 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 5511 p.Ser91Tyr missense_variant 0.33
gyrB 6214 c.975G>A synonymous_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 763251 c.-119C>T upstream_gene_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 1.0
fbiC 1303257 c.327C>T synonymous_variant 0.33
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475130 n.1473A>T non_coding_transcript_exon_variant 0.67
fabG1 1673380 c.-60C>G upstream_gene_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101821 p.Lys408Glu missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169392 c.1221C>T synonymous_variant 0.13
PPE35 2169728 c.885C>T synonymous_variant 0.5
PPE35 2169744 p.Ala290Gly missense_variant 0.5
PPE35 2169746 p.Ile289Phe missense_variant 0.5
PPE35 2169749 c.864A>C synonymous_variant 0.5
PPE35 2169759 p.Gly285Tyr missense_variant 0.67
PPE35 2169762 p.Ile284Ser missense_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289407 c.-166G>A upstream_gene_variant 0.67
kasA 2519140 c.1026G>C synonymous_variant 0.4
kasA 2519143 c.1029G>C synonymous_variant 0.4
eis 2715575 c.-243G>A upstream_gene_variant 0.4
ald 3086947 p.Ser43* stop_gained 0.4
alr 3841612 c.-193_-192insC upstream_gene_variant 0.18
clpC1 4039443 p.Leu421Pro missense_variant 0.67
embC 4240161 p.Thr100Ile missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0