TB-Profiler result

Run: ERR3148160
Summary

Run ID: ERR3148160

Sample name:

Date: 15-08-2022 11:51:38

Number of reads: 1004698

Percentage reads mapped: 99.41

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.99
lineage4.1.1.3 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
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288883 p.Leu120Pro missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491647 p.Asp289Asn missense_variant 0.12
rpoB 760760 c.954C>A synonymous_variant 0.17
rpoC 763746 p.Glu126Gly missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765609 p.Asp747Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778853 p.Val18Asp missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674428 p.Gly76Ala missense_variant 0.12
rpsA 1833727 c.186G>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155784 p.Ala110Thr missense_variant 0.15
PPE35 2169632 c.981C>A synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290232 c.-991G>T upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612125 p.Val331Gly missense_variant 0.12
Rv3236c 3613212 c.-99_-97delGCC upstream_gene_variant 0.13
fbiB 3642825 p.Glu431* stop_gained 0.15
ddn 3986645 c.-199G>T upstream_gene_variant 0.13
embC 4242332 p.Gly824Trp missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243920 p.Gly230Ser missense_variant 1.0
embA 4244290 p.Gly353Val missense_variant 0.2
embA 4245408 p.Leu726Val missense_variant 0.09
embB 4247695 c.1182G>A synonymous_variant 0.19
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267688 c.1149G>T synonymous_variant 0.13
ubiA 4269742 p.Leu31Pro missense_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 0.12
ethA 4328351 c.-878C>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 0.43
gid 4407713 p.Gly164Arg missense_variant 1.0