TB-Profiler result

Run: ERR046903
Summary

Run ID: ERR046903

Sample name:

Date: 31-03-2023 08:56:32

Number of reads: 8790835

Percentage reads mapped: 99.75

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 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 0.99 pyrazinamide
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
ethA 4326231 c.1242delT frameshift_variant 0.99 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
fgd1 491027 p.Asn82Thr missense_variant 0.18
rpoB 759620 c.-187A>C upstream_gene_variant 0.33
rpoC 762836 c.-534C>G upstream_gene_variant 0.33
rpoC 764725 p.Phe452Leu missense_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.18
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 0.17
inhA 1674892 p.Asn231Asp missense_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.2
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169379 p.Phe412Val missense_variant 0.17
PPE35 2169866 c.747G>C synonymous_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518891 c.777C>A synonymous_variant 0.19
eis 2714366 p.Val323Leu missense_variant 0.29
eis 2715586 c.-254G>C upstream_gene_variant 0.26
ahpC 2725954 c.-239C>T upstream_gene_variant 0.24
ahpC 2726151 c.-42T>C upstream_gene_variant 0.99
folC 2746186 c.1413G>C synonymous_variant 0.28
folC 2747478 p.Thr41Pro missense_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.18
Rv2752c 3064552 p.Arg547Pro missense_variant 0.23
Rv2752c 3064741 p.Gly484Ala missense_variant 0.32
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.8
fprA 3474601 p.Arg199Gly missense_variant 0.25
fbiB 3641955 p.Gly141Arg missense_variant 0.25
fbiB 3642734 c.1200G>C synonymous_variant 0.18
rpoA 3878238 p.Asp90Glu missense_variant 0.14
rpoA 3878641 c.-135delG upstream_gene_variant 0.12
ddn 3987013 p.Gly57Ala missense_variant 0.2
clpC1 4039729 p.Asp326Asn missense_variant 0.99
clpC1 4039932 p.Gly258Val missense_variant 0.35
panD 4043905 p.Glu126Val missense_variant 0.99
embC 4241456 p.Ala532Pro missense_variant 0.43
embC 4242476 p.Pro872Ala missense_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.39
embA 4243977 p.Ala249Pro missense_variant 0.24
embA 4244375 c.1143C>G synonymous_variant 0.2
embB 4248725 p.Ser738Ala missense_variant 0.28
ubiA 4269529 p.Ala102Gly missense_variant 0.27
ethA 4327672 c.-199G>A upstream_gene_variant 0.29
ethR 4327912 p.Arg122Gly missense_variant 0.21
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