TB-Profiler result

Run: ERR2514881
Summary

Run ID: ERR2514881

Sample name:

Date: 31-03-2023 20:37:19

Number of reads: 765180

Percentage reads mapped: 99.73

Strain: lineage4.3.3

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 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
katG 2154389 c.1721_1722dupCG frameshift_variant 0.11 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762451 p.Arg882Leu missense_variant 0.11
rpoC 764202 p.Arg278Gln missense_variant 0.13
rpoC 764274 p.Phe302Ser missense_variant 0.12
rpoC 764298 p.Met310Thr missense_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766136 p.Arg923Trp missense_variant 0.12
rpoC 766667 p.Ser1100Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304477 p.Ala516Glu missense_variant 0.13
Rv1258c 1406440 p.Ala301Thr missense_variant 0.11
atpE 1461108 p.Ile22Leu missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472229 n.384C>T non_coding_transcript_exon_variant 0.4
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.25
inhA 1674026 c.-176A>C upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168044 p.Ala857Thr missense_variant 0.1
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.27
PPE35 2170066 p.Ala183Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289525 c.-284G>C upstream_gene_variant 0.1
pncA 2290063 c.-822G>T upstream_gene_variant 0.11
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746516 c.1083T>C synonymous_variant 0.12
ribD 2987480 c.642G>A synonymous_variant 1.0
thyX 3067708 p.Phe80Leu missense_variant 0.17
thyX 3068087 c.-142C>A upstream_gene_variant 0.13
thyX 3068090 c.-145T>C upstream_gene_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339421 p.Val102Leu missense_variant 0.18
fbiD 3339490 p.Leu125Ile missense_variant 1.0
fbiD 3339672 c.555G>T synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612995 p.Leu41Ser missense_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039011 p.Ala565Val missense_variant 0.11
clpC1 4039484 c.1221T>G synonymous_variant 0.14
embC 4240522 c.660C>T synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245205 p.Gly658Glu missense_variant 0.14
embB 4247636 p.Pro375Ser missense_variant 0.11
aftB 4267098 p.Ala580Gly missense_variant 0.15
aftB 4267220 c.1617C>T synonymous_variant 0.11
aftB 4267790 c.1046delC frameshift_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0