TB-Profiler result

Run: ERR10867783
Summary

Run ID: ERR10867783

Sample name:

Date: 31-03-2023 11:20:55

Number of reads: 1187064

Percentage reads mapped: 99.71

Strain: lineage4.8

Drug-resistance: MDR-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 0.99
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
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.97 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289057 p.Pro62Leu missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile 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
ccsA 620135 p.Ala82Val missense_variant 0.14
ccsA 620204 p.Val105Ala missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472870 n.1025T>A non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156283 c.-172G>C upstream_gene_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.22
PPE35 2170053 p.Thr187Ser missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223316 c.-152T>C upstream_gene_variant 0.18
Rv1979c 2223320 c.-156T>C upstream_gene_variant 0.17
Rv1979c 2223321 c.-157G>A upstream_gene_variant 0.17
Rv1979c 2223325 c.-161G>A upstream_gene_variant 0.21
pepQ 2859720 p.Met233Ile missense_variant 0.11
fbiB 3640815 c.-720A>G upstream_gene_variant 0.1
rpoA 3878567 c.-60C>G upstream_gene_variant 0.21
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.21
embB 4246548 p.Pro12Gln missense_variant 0.21
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4246563 p.Leu17Trp missense_variant 0.21
embB 4246567 c.54G>T synonymous_variant 0.24
embB 4249735 c.3222T>C synonymous_variant 0.13
aftB 4268812 p.Ser9Pro missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407917 p.Arg96Cys missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0