TB-Profiler result

Run: ERR046944
Summary

Run ID: ERR046944

Sample name:

Date: 31-03-2023 08:57:53

Number of reads: 5260733

Percentage reads mapped: 99.77

Strain: lineage4.8

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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 7521 p.Ala74Ser missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289253 c.-12T>C upstream_gene_variant 1.0 pyrazinamide
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
ethA 4326231 c.1242delT frameshift_variant 1.0 ethionamide, ethionamide
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
mshA 575932 p.Glu195Asp missense_variant 0.19
rpoC 762836 c.-534C>G upstream_gene_variant 0.23
rpoC 764725 p.Phe452Leu missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 0.98
mmpL5 777399 p.Thr361Arg missense_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800997 p.Asn63Lys missense_variant 0.38
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.18
rrl 1476408 n.2751G>C non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.24
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.46
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.3
ahpC 2726151 c.-42T>C upstream_gene_variant 1.0
folC 2747478 p.Thr41Pro missense_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.3
Rv2752c 3064552 p.Arg547Pro missense_variant 0.21
Rv2752c 3064741 p.Gly484Ala missense_variant 0.25
thyX 3067995 c.-50A>C upstream_gene_variant 0.25
thyA 3073806 c.666C>G synonymous_variant 0.23
fbiD 3339273 c.156T>G synonymous_variant 0.24
fbiD 3339550 p.Gly145Trp missense_variant 0.21
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3475280 p.Val425Gly missense_variant 0.35
fbiB 3642772 p.Asp413Ala missense_variant 0.23
rpoA 3878238 p.Asp90Glu missense_variant 0.19
ddn 3987013 p.Gly57Ala missense_variant 0.22
clpC1 4038857 c.1848C>A synonymous_variant 0.2
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4039932 p.Gly258Val missense_variant 0.26
panD 4043905 p.Glu126Val missense_variant 1.0
embC 4239842 c.-21C>A upstream_gene_variant 0.24
embC 4241456 p.Ala532Pro missense_variant 0.37
embC 4242476 p.Pro872Ala missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.28
ethA 4327672 c.-199G>A upstream_gene_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408061 p.His48Asn missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0