TB-Profiler result

Run: ERR028618
Summary

Run ID: ERR028618

Sample name:

Date: 31-03-2023 08:24:47

Number of reads: 875362

Percentage reads mapped: 99.44

Strain: lineage4.1.2.1

Drug-resistance: HR-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
lineage4.1 Euro-American T;X;H None 0.49
lineage4.1.2 Euro-American T;H None 0.54
lineage4.3.4 Euro-American (LAM) LAM RD174 0.08
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.2
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
inhA 1674048 c.-154G>A upstream_gene_variant 0.23 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.14 isoniazid
embB 4247429 p.Met306Val missense_variant 0.12 ethambutol
ethA 4326130 c.1343delA frameshift_variant 0.22 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.43
mshA 575679 p.Asn111Ser missense_variant 0.5
rpoB 760115 c.309C>T synonymous_variant 0.65
rpoC 763031 c.-339T>C upstream_gene_variant 0.19
rpoC 764995 c.1626C>G synonymous_variant 0.5
rpoC 765150 p.Gly594Glu missense_variant 0.55
rpoC 767314 p.Tyr1315* stop_gained 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778144 p.Ile113Val missense_variant 0.2
mmpS5 778743 p.Val55Met missense_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.24
rpsA 1834177 c.636A>C synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.23
Rv1979c 2223057 c.108A>G synonymous_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.27
eis 2714366 p.Val323Leu missense_variant 0.25
ahpC 2726323 p.Pro44Arg missense_variant 0.14
folC 2747263 c.336C>A synonymous_variant 0.3
thyA 3073868 p.Thr202Ala missense_variant 0.36
thyA 3074657 c.-186C>G upstream_gene_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 0.9
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.83
Rv3236c 3612009 p.Ala370Thr missense_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 0.14
fbiB 3642772 p.Asp413Ala missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.38
clpC1 4038496 p.Arg737Trp missense_variant 0.2
clpC1 4039932 p.Gly258Val missense_variant 0.43
embC 4242425 p.Arg855Gly missense_variant 0.6
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.31
embA 4242883 c.-350C>G upstream_gene_variant 0.25
embA 4243460 c.228C>T synonymous_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 0.5
ubiA 4269529 p.Ala102Gly missense_variant 0.42
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.31