TB-Profiler result

Run: SRR4034204
Summary

Run ID: SRR4034204

Sample name:

Date: 04-04-2023 06:38:07

Number of reads: 598653

Percentage reads mapped: 99.59

Strain: lineage4.3.2.1

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 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.98
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 2155187 p.Gly309Ser missense_variant 0.15 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 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7397 c.96G>A synonymous_variant 0.2
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8885 c.1584C>A synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.5
ccsA 620017 p.Gly43* stop_gained 0.17
rpoB 761871 p.Arg689* stop_gained 0.25
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766788 p.Glu1140Gly missense_variant 0.13
mmpL5 775619 c.2862G>A synonymous_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775834 p.Ala883Thr missense_variant 0.17
mmpR5 778226 c.-764T>C upstream_gene_variant 0.15
mmpS5 778602 c.303delC frameshift_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417303 c.45G>A synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
inhA 1674918 c.717C>T synonymous_variant 0.14
tlyA 1917752 c.-188C>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918209 c.270C>T synonymous_variant 0.2
tlyA 1918669 p.Arg244Cys missense_variant 0.12
katG 2153970 p.Asp714Glu missense_variant 0.3
katG 2154108 p.Trp668Cys missense_variant 0.25
PPE35 2168813 c.1800C>A synonymous_variant 0.14
PPE35 2170601 c.12A>T synonymous_variant 0.18
Rv1979c 2221792 p.Val458Glu missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288909 p.Glu111Asp missense_variant 0.18
eis 2714311 p.Thr341Asn missense_variant 0.12
eis 2715095 p.Ala80Thr missense_variant 0.17
pepQ 2859827 p.Ala198Thr missense_variant 0.22
ribD 2987138 c.300C>A synonymous_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087524 c.705G>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474649 c.643C>T synonymous_variant 0.18
fprA 3475183 p.Ala393Thr missense_variant 0.13
Rv3236c 3613149 c.-35_-34delCG upstream_gene_variant 0.18
fbiB 3641996 c.462C>G synonymous_variant 0.2
alr 3840595 p.Thr276Ser missense_variant 0.17
rpoA 3877798 p.Ser237Leu missense_variant 0.22
ddn 3987295 p.Pro151Leu missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039572 p.Ala378Val missense_variant 0.18
clpC1 4040520 p.Gln62Arg missense_variant 0.17
embC 4240693 c.831T>C synonymous_variant 1.0
embC 4242078 p.Ser739Tyr missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243791 p.Ala187Thr missense_variant 0.2
embA 4244841 p.Arg537Trp missense_variant 0.13
embB 4248216 p.Arg568Leu missense_variant 0.14
embB 4249786 c.3273G>A synonymous_variant 0.22
aftB 4267139 c.1698G>A synonymous_variant 0.17
ethA 4328333 c.-860C>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0