TB-Profiler result

Run: ERR2653104
Summary

Run ID: ERR2653104

Sample name:

Date: 31-03-2023 22:31:38

Number of reads: 594426

Percentage reads mapped: 99.18

Strain: lineage4.1.1

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
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 761101 p.Gln432Pro missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288957 p.Tyr95* stop_gained 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_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
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801267 c.459A>G synonymous_variant 1.0
fbiC 1303722 c.792C>A synonymous_variant 0.11
Rv1258c 1406776 c.564delT frameshift_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.11
PPE35 2170053 p.Thr187Ser missense_variant 0.12
Rv1979c 2222483 p.Ala228Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726210 c.18T>C synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087854 c.1035G>A synonymous_variant 1.0
fbiD 3339175 p.Ala20Thr missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641447 p.Thr302Met missense_variant 1.0
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3877960 p.Val183Gly missense_variant 0.95
rpoA 3878555 c.-48G>A upstream_gene_variant 0.11
rpoA 3878559 c.-53_-52insC upstream_gene_variant 0.17
rpoA 3878599 c.-92C>G upstream_gene_variant 0.18
rpoA 3878601 c.-95delG upstream_gene_variant 0.3
rpoA 3878613 c.-113_-107delCAACCCA upstream_gene_variant 0.27
panD 4043932 p.Met117Thr missense_variant 0.11
panD 4044050 p.Leu78Val missense_variant 0.12
embC 4240897 c.1035C>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269307 p.Phe176Ser missense_variant 0.94
ethA 4326908 p.Thr189Lys missense_variant 1.0
ethR 4327586 p.Arg13Met missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0