TB-Profiler result

Run: ERR2229538
Summary

Run ID: ERR2229538

Sample name:

Date: 31-03-2023 17:18:12

Number of reads: 1201117

Percentage reads mapped: 99.31

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 2155483 c.628delT frameshift_variant 0.12 isoniazid
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 576108 p.Ala254Gly missense_variant 0.27
mshA 576292 c.945C>A synonymous_variant 0.15
mshA 576350 p.Asp335Tyr missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777481 p.Thr334Ser missense_variant 0.12
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
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673349 c.-91G>C upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.34
rpsA 1834349 p.Glu270* stop_gained 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155312 p.Val267Asp missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.17
PPE35 2169272 c.1341C>G synonymous_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.19
PPE35 2170053 p.Thr187Ser missense_variant 0.19
Rv1979c 2222285 p.Ala294Thr missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518147 p.Phe11Leu missense_variant 0.12
kasA 2518195 c.81G>A synonymous_variant 0.12
kasA 2518612 c.498C>T synonymous_variant 0.12
kasA 2519140 c.1026G>C synonymous_variant 0.14
kasA 2519143 c.1029G>C synonymous_variant 0.14
eis 2714200 p.Lys378Arg missense_variant 0.1
pepQ 2859601 c.817delG frameshift_variant 0.12
pepQ 2860159 p.Ala87Gly missense_variant 0.15
ribD 2987449 p.Glu204Val missense_variant 0.18
Rv2752c 3066126 c.66C>T synonymous_variant 0.11
whiB7 3568430 p.Gly84Arg missense_variant 0.18
fbiB 3642245 c.711C>A synonymous_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.15
ddn 3987010 p.Thr56Asn missense_variant 0.21
embC 4241613 p.Thr584Ile missense_variant 0.18
embC 4241635 c.1773G>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244768 p.Glu512Asp missense_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.4
embB 4246567 c.54_55insT frameshift_variant 0.67
embB 4247028 p.Leu172Arg missense_variant 0.6
embB 4247066 p.Ile185Val missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0