TB-Profiler result

Run: ERR6358742
Summary

Run ID: ERR6358742

Sample name:

Date: 02-04-2023 02:12:08

Number of reads: 7002996

Percentage reads mapped: 99.62

Strain: lineage4.6.1.2;lineage4.2.2.2

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.6 Euro-American T;LAM None 0.71
lineage4.2 Euro-American H;T;LAM None 0.31
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.3
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.7
lineage4.6.1.2 Euro-American T2 RD724 0.69
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.31
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 0.79 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.69 isoniazid
pncA 2289114 p.His43Pro missense_variant 0.69 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.7 ethambutol
ethA 4326249 c.1215_1224delGTTGAATTAC frameshift_variant 0.63 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
gyrA 7539 p.Thr80Ala missense_variant 0.66
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 0.32
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 0.31
mshA 576108 p.Ala254Gly missense_variant 0.24
rpoB 761489 c.1683G>A synonymous_variant 0.32
rpoC 764660 p.Val431Met missense_variant 0.68
rpoC 764810 p.Pro481Thr missense_variant 0.72
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 0.7
embR 1417485 c.-138T>G upstream_gene_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170692 c.-80T>G upstream_gene_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288800 p.Arg148Cys missense_variant 0.3
eis 2714308 p.Pro342Leu missense_variant 0.65
Rv2752c 3065920 p.Pro91Leu missense_variant 0.67
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.33
ald 3086742 c.-78A>C upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 0.26
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 0.74
embB 4246584 p.Arg24Pro missense_variant 0.2
ubiA 4269124 p.Ala237Val missense_variant 0.69
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408094 p.Gly37Arg missense_variant 0.68