TB-Profiler result

Run: ERR2229617
Summary

Run ID: ERR2229617

Sample name:

Date: 31-03-2023 17:21:56

Number of reads: 1260644

Percentage reads mapped: 99.14

Strain: lineage4.8

Drug-resistance: Sensitive

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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
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 6077 p.Gly280Ser missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776069 c.2412C>T synonymous_variant 0.17
mmpL5 776742 p.Pro580His missense_variant 0.12
mmpL5 777098 c.1383C>T synonymous_variant 0.11
mmpL5 777119 p.His454Gln missense_variant 0.17
mmpL5 777122 c.1359C>T synonymous_variant 0.19
mmpL5 777313 p.Pro390Ser 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
rrl 1474078 n.421G>A non_coding_transcript_exon_variant 0.13
rrl 1474565 n.908T>C non_coding_transcript_exon_variant 0.2
rrl 1474809 n.1152T>C non_coding_transcript_exon_variant 0.13
rrl 1476378 n.2721C>A non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103113 c.-71C>T upstream_gene_variant 0.12
katG 2154118 p.Gly665Val missense_variant 0.2
katG 2154165 c.1947C>T synonymous_variant 0.15
PPE35 2167814 c.2799C>T synonymous_variant 0.23
PPE35 2167865 c.2748G>C synonymous_variant 0.14
PPE35 2167868 c.2745A>C synonymous_variant 0.19
PPE35 2168243 p.Ser790Arg missense_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.31
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289744 c.-503G>C upstream_gene_variant 0.12
pncA 2289750 c.-509C>T upstream_gene_variant 0.12
kasA 2519140 c.1026G>C synonymous_variant 0.15
kasA 2519143 c.1029G>C synonymous_variant 0.16
pepQ 2860130 p.Phe97Leu missense_variant 0.14
Rv3236c 3612969 p.Gly50Trp missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.13
embB 4246548 p.Pro12Gln missense_variant 0.35
embB 4246555 c.42G>C synonymous_variant 0.46
embB 4246556 p.Ala15Pro missense_variant 0.46
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.4
embB 4246584 p.Arg24Pro missense_variant 0.29
ethA 4326347 p.Gly376Val missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0