TB-Profiler result

Run: ERR046786
Summary

Run ID: ERR046786

Sample name:

Date: 31-03-2023 08:51:11

Number of reads: 6054715

Percentage reads mapped: 98.17

Strain: lineage4.1.1.3.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 1.0
lineage4.1.1.3.1 Euro-American (X-type) X1;X3 RD193 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 761277 p.Ile491Phe missense_variant 1.0 rifampicin
katG 2154695 p.Val473Phe missense_variant 0.85 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575309 c.-39C>G upstream_gene_variant 0.22
mshA 576751 p.Lys468Asn missense_variant 0.16
rpoB 759620 c.-187A>C upstream_gene_variant 0.27
rpoC 762836 c.-534C>G upstream_gene_variant 0.33
rpoC 764725 p.Phe452Leu missense_variant 0.24
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.23
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303601 p.Glu224Gly missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.25
PPE35 2169866 c.747G>C synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
eis 2714366 p.Val323Leu missense_variant 0.28
ahpC 2725954 c.-239C>T upstream_gene_variant 0.24
ahpC 2726737 p.Asp182Ala missense_variant 0.2
folC 2746186 c.1413G>C synonymous_variant 0.21
pepQ 2859381 c.1038C>G synonymous_variant 0.22
Rv2752c 3064741 p.Gly484Ala missense_variant 0.35
thyX 3067995 c.-50A>C upstream_gene_variant 0.17
thyA 3073806 c.666C>G synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Gly missense_variant 0.21
fbiB 3641955 p.Gly141Arg missense_variant 0.19
fbiB 3642734 c.1200G>C synonymous_variant 0.18
fbiB 3642772 p.Asp413Ala missense_variant 0.16
alr 3840268 p.Thr385Pro missense_variant 0.27
rpoA 3878641 c.-135delG upstream_gene_variant 0.11
clpC1 4038857 c.1848C>A synonymous_variant 0.3
clpC1 4039363 p.Ala448Pro missense_variant 0.22
clpC1 4039932 p.Gly258Val missense_variant 0.33
embC 4241056 c.1194C>G synonymous_variant 0.27
embC 4242476 p.Pro872Ala missense_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.24
embA 4244375 c.1143C>G synonymous_variant 0.18
embB 4246585 c.72C>G synonymous_variant 0.18
embB 4248725 p.Ser738Ala missense_variant 0.28
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.16
aftB 4269540 c.-704C>T upstream_gene_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.23
ethR 4327912 p.Arg122Gly missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0