TB-Profiler result

Run: ERR2229118
Summary

Run ID: ERR2229118

Sample name:

Date: 31-03-2023 16:41:01

Number of reads: 610698

Percentage reads mapped: 99.49

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
pncA 2288703 p.Val180Ala missense_variant 0.11 pyrazinamide
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 7321 p.Pro7Leu missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.27
mshA 576424 c.1077T>C synonymous_variant 0.15
ccsA 619916 p.Gly9Val missense_variant 0.4
rpoB 759721 c.-86G>A upstream_gene_variant 0.22
rpoB 760432 p.Asp209Gly missense_variant 0.11
rpoB 760696 p.Glu297Val missense_variant 0.18
rpoB 762207 p.Thr801Ala missense_variant 0.25
rpoC 762506 c.-864C>T upstream_gene_variant 0.22
rpoC 764865 p.Asn499Ile missense_variant 0.15
rpoC 765953 p.Asp862His missense_variant 0.11
rpoC 766177 c.2808C>T synonymous_variant 0.2
rpoC 766857 p.Arg1163Leu missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776080 p.Ala801Ser missense_variant 0.17
mmpL5 776081 c.2400G>A synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800730 c.-79A>G upstream_gene_variant 0.11
rplC 801428 c.622delG frameshift_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1407235 c.104_105delTG frameshift_variant 0.15
Rv1258c 1407243 p.Leu33Gln missense_variant 0.14
Rv1258c 1407521 c.-181C>A upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473496 n.-162G>A upstream_gene_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.33
fabG1 1673681 p.Pro81Leu missense_variant 0.15
inhA 1674638 p.Gly146Val missense_variant 0.33
rpsA 1834605 p.Arg355His missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102788 c.255G>T synonymous_variant 0.15
PPE35 2167955 c.2658A>C synonymous_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.14
PPE35 2167967 c.2646A>C synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169879 p.Phe245Ser missense_variant 0.1
PPE35 2169902 p.Leu237Phe missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.12
PPE35 2170053 p.Thr187Ser missense_variant 0.12
Rv1979c 2222873 p.His98Tyr missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289416 c.-175T>A upstream_gene_variant 0.14
pncA 2289574 c.-333T>C upstream_gene_variant 0.18
kasA 2518606 c.492G>C synonymous_variant 0.17
kasA 2518609 p.Met165Ile missense_variant 0.17
kasA 2518879 c.765A>G synonymous_variant 0.2
kasA 2518882 c.768C>A synonymous_variant 0.2
folC 2747618 c.-20A>G upstream_gene_variant 0.17
pepQ 2860298 p.Gly41Ser missense_variant 0.2
ribD 2987084 c.246G>T synonymous_variant 0.17
Rv2752c 3066027 c.165C>G synonymous_variant 0.14
thyX 3067340 c.606G>A synonymous_variant 0.22
thyA 3074571 c.-100T>C upstream_gene_variant 0.12
thyA 3074580 c.-109T>C upstream_gene_variant 0.12
ald 3087665 c.846C>A synonymous_variant 0.15
Rv3236c 3612362 p.Thr252Ile missense_variant 0.17
fbiB 3642215 c.681G>C synonymous_variant 0.25
fbiB 3642753 c.1219C>T synonymous_variant 0.15
alr 3841348 c.72delC frameshift_variant 0.14
clpC1 4039682 c.1023C>T synonymous_variant 0.15
clpC1 4040085 p.Arg207His missense_variant 0.12
clpC1 4040231 c.474C>A synonymous_variant 0.15
embC 4239689 c.-174C>T upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.83
embB 4246555 c.42G>C synonymous_variant 1.0
embB 4246556 p.Ala15Pro missense_variant 1.0
ubiA 4269232 p.Arg201His missense_variant 0.13
ethR 4326691 c.-858C>A upstream_gene_variant 0.13
ethR 4326877 c.-672G>T upstream_gene_variant 0.25
ethR 4327315 c.-234A>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0