TB-Profiler result

Run: ERR046788
Summary

Run ID: ERR046788

Sample name:

Date: 31-03-2023 08:51:13

Number of reads: 6585811

Percentage reads mapped: 98.31

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 0.56 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 576751 p.Lys468Asn missense_variant 0.21
rpoB 759620 c.-187A>C upstream_gene_variant 0.28
rpoC 762836 c.-534C>G upstream_gene_variant 0.28
rpoC 764725 p.Phe452Leu missense_variant 0.19
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767305 p.Tyr1312* stop_gained 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303601 p.Glu224Gly missense_variant 1.0
Rv1258c 1406358 p.Ile328Thr missense_variant 0.16
atpE 1461019 c.-26C>A upstream_gene_variant 0.15
rrs 1471658 n.-188T>G upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.24
katG 2156110 p.Val1Gly missense_variant 0.35
PPE35 2167871 c.2742G>C synonymous_variant 0.24
PPE35 2169379 p.Phe412Val missense_variant 0.18
PPE35 2169866 c.747G>C synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.22
eis 2715586 c.-254G>C upstream_gene_variant 0.36
folC 2746186 c.1413G>C synonymous_variant 0.19
Rv2752c 3064552 p.Arg547Pro missense_variant 0.2
thyX 3067995 c.-50A>C upstream_gene_variant 0.17
thyA 3073806 c.666C>G synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475280 p.Val425Gly missense_variant 0.19
fbiB 3642512 p.Leu326Phe missense_variant 0.16
ddn 3987013 p.Gly57Ala missense_variant 0.18
clpC1 4039932 p.Gly258Val missense_variant 0.34
embC 4241056 c.1194C>G synonymous_variant 0.19
embC 4241456 p.Ala532Pro missense_variant 0.42
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
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.29
aftB 4269540 c.-704C>T upstream_gene_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.34
ethR 4327912 p.Arg122Gly missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0