TB-Profiler result

Run: ERR8774256

Summary

Run ID: ERR8774256

Sample name:

Date: 02-04-2023 08:25:45

Number of reads: 494606

Percentage reads mapped: 99.68

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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 761102 c.1297_1299dupTTC conservative_inframe_insertion 1.0 rifampicin, rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
gyrB 5743 c.504G>T synonymous_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9453 p.Arg718Cys missense_variant 0.14
fgd1 491064 c.282A>G synonymous_variant 0.2
rpoC 765927 p.Thr853Asn missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406255 p.Leu362Phe missense_variant 0.13
Rv1258c 1407021 p.Ala107Asp missense_variant 0.12
embR 1417264 c.84G>A synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673923 p.Gly162Cys missense_variant 0.18
inhA 1674687 c.486G>T synonymous_variant 0.18
inhA 1674988 p.Gly263Cys missense_variant 0.22
rpsA 1833441 c.-101C>A upstream_gene_variant 0.13
rpsA 1833962 p.Asp141Tyr missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102028 p.Gly339Trp missense_variant 0.12
katG 2155389 c.723C>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714956 p.Tyr126Cys missense_variant 0.15
thyX 3067474 p.Pro158Ala missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
Rv3083 3449331 c.828C>A synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474861 p.Glu285Asp missense_variant 0.15
fprA 3475017 c.1011G>A synonymous_variant 0.12
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612869 c.247delG frameshift_variant 0.14
fbiA 3640778 p.Trp79Leu missense_variant 0.18
fbiB 3642750 p.Asp406Tyr missense_variant 0.12
clpC1 4038443 c.2262G>A synonymous_variant 0.14
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246683 p.Asp57Gly missense_variant 0.14
embB 4248166 c.1653C>T synonymous_variant 0.13
embB 4249166 p.Gly885Ser missense_variant 0.29
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0