TB-Profiler result

Run: ERR2229071
Summary

Run ID: ERR2229071

Sample name:

Date: 31-03-2023 16:36:56

Number of reads: 948755

Percentage reads mapped: 99.45

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 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
mmpR5 779191 p.Ser68Gly missense_variant 0.12 clofazimine, bedaquiline
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
fgd1 491097 c.315G>A synonymous_variant 0.13
mshA 576108 p.Ala254Gly missense_variant 0.5
rpoB 760375 p.Asp190Val missense_variant 0.18
rpoC 764495 p.Glu376* stop_gained 0.2
rpoC 765996 p.Arg876Leu missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776854 p.Thr543Ala missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302860 c.-71G>T upstream_gene_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304113 p.Gln395Lys missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475014 n.1357A>T non_coding_transcript_exon_variant 0.29
fabG1 1673357 c.-83G>A upstream_gene_variant 0.2
fabG1 1673359 c.-81T>C upstream_gene_variant 0.22
fabG1 1673361 c.-79C>G upstream_gene_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169732 p.Asn294Ser missense_variant 0.18
PPE35 2169748 p.Ile289Phe missense_variant 0.12
PPE35 2169749 c.864A>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.45
PPE35 2170053 p.Thr187Ser missense_variant 0.46
PPE35 2170159 p.Ala152Ser missense_variant 0.12
PPE35 2170232 c.381T>C synonymous_variant 0.1
PPE35 2170235 c.378T>C synonymous_variant 0.1
PPE35 2170238 c.375T>G synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289961 c.-720C>A upstream_gene_variant 0.11
folC 2747493 p.Gln36Lys missense_variant 0.13
pepQ 2859481 p.Ala313Val missense_variant 0.14
pepQ 2860104 p.Asp105Glu missense_variant 0.2
ribD 2987582 c.744C>T synonymous_variant 0.12
thyX 3067340 c.606G>A synonymous_variant 0.19
ald 3087105 p.His96Asp missense_variant 0.12
ald 3087269 p.Met150Ile missense_variant 0.14
fprA 3474817 p.Phe271Ile missense_variant 0.14
fprA 3475231 p.Trp409Arg missense_variant 0.15
Rv3236c 3612870 p.Ala83Ser missense_variant 0.13
clpC1 4038888 p.Glu606Ala missense_variant 0.29
clpC1 4038896 c.1809C>A synonymous_variant 0.29
clpC1 4038899 c.1806C>G synonymous_variant 0.29
clpC1 4038902 c.1803C>T synonymous_variant 0.29
clpC1 4038905 c.1800A>C synonymous_variant 0.29
clpC1 4038914 c.1791G>C synonymous_variant 0.25
clpC1 4039062 p.Ser548Trp missense_variant 0.11
embC 4241364 p.Leu501Pro missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243484 c.252C>A synonymous_variant 0.13
embA 4244326 p.Gly365Val missense_variant 0.17
embA 4244749 p.Thr506Ile missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.13
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4249262 p.Val917Leu missense_variant 0.12
embB 4249535 p.Glu1008Lys missense_variant 0.13
aftB 4267937 c.900G>A synonymous_variant 0.4
aftB 4268022 p.Leu272Gln missense_variant 0.29
aftB 4269270 c.-434G>A upstream_gene_variant 0.12
ethA 4327512 c.-39T>C upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0