TB-Profiler result

Run: ERR4797074
Summary

Run ID: ERR4797074

Sample name:

Date: 01-04-2023 07:20:42

Number of reads: 5373302

Percentage reads mapped: 98.92

Strain: lineage4.8

Drug-resistance: Pre-XDR-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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155342 p.Met257Thr missense_variant 0.12 isoniazid
pncA 2288844 p.Ile133Thr missense_variant 1.0 pyrazinamide
folC 2747471 p.Ile43Thr missense_variant 1.0 para-aminosalicylic_acid
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
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 490756 c.-27T>G upstream_gene_variant 0.21
mshA 576442 p.Cys365Trp missense_variant 0.21
ccsA 620300 p.Leu137Arg missense_variant 0.16
rpoB 761119 p.Asn438Ser missense_variant 0.15
rpoB 763151 p.Phe1115Leu missense_variant 0.22
rpoC 764367 p.Gly333Ala missense_variant 0.17
rpoC 764431 c.1062G>A synonymous_variant 0.12
rpoC 766466 p.Glu1033Lys missense_variant 1.0
rpoC 766867 c.3498C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776710 p.Cys591Arg missense_variant 0.12
mmpL5 778051 p.Gly144Cys missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800999 p.Lys64Arg missense_variant 0.11
fbiC 1303134 c.204G>C synonymous_variant 0.12
embR 1416996 p.Glu118* stop_gained 0.6
embR 1417541 c.-194A>G upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471788 n.-58G>T upstream_gene_variant 0.44
rrs 1471793 n.-53G>T upstream_gene_variant 0.5
rrs 1471805 n.-41C>A upstream_gene_variant 0.67
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.17
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.13
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.13
fabG1 1673553 p.Asp38Glu missense_variant 0.38
fabG1 1673558 p.His40Pro missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102938 c.105G>A synonymous_variant 0.14
katG 2154606 c.1506A>G synonymous_variant 0.1
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169653 c.960A>T synonymous_variant 0.12
PPE35 2170386 p.Leu76Arg missense_variant 0.23
PPE35 2170495 p.Ser40Ala missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289818 c.-577T>C upstream_gene_variant 0.12
pncA 2289954 c.-713A>G upstream_gene_variant 0.11
kasA 2519071 p.Asp319Glu missense_variant 0.23
eis 2715140 p.Met65Leu missense_variant 0.14
thyA 3073755 c.717C>T synonymous_variant 0.1
fprA 3474216 c.210G>A synonymous_variant 0.2
whiB7 3568733 c.-54T>A upstream_gene_variant 0.11
rpoA 3878135 p.Ile125Leu missense_variant 0.11
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4240061 p.Phe67Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267400 c.1437G>C synonymous_variant 0.19
aftB 4267902 p.Val312Ala missense_variant 0.14
aftB 4268619 p.Val73Gly missense_variant 0.37
whiB6 4338200 p.Asp108His missense_variant 0.22
whiB6 4338205 p.Val106Gly missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407670 p.Met178Arg missense_variant 1.0
ald 3086364 c.-455_*2032del transcript_ablation 1.0