TB-Profiler result

Run: ERR4814437
Summary

Run ID: ERR4814437

Sample name:

Date: 01-04-2023 13:17:41

Number of reads: 906354

Percentage reads mapped: 99.34

Strain: lineage4.1.2.1

Drug-resistance: Other

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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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
tlyA 1917940 c.2delT frameshift_variant 0.12 capreomycin
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 8906 c.1605C>A synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491316 c.534C>G synonymous_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 619864 c.-27G>A upstream_gene_variant 0.2
ccsA 620855 p.Gly322Val missense_variant 1.0
rpoB 759852 p.Ser16Cys missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761152 p.Leu449Gln missense_variant 0.19
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776092 p.Ser797Arg missense_variant 0.1
mmpL5 777824 p.Leu219Phe missense_variant 1.0
mmpL5 778242 p.Lys80Met missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.35
embR 1416786 p.Ser188Gly missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102389 c.654G>C synonymous_variant 0.25
ndh 2102392 c.651C>A synonymous_variant 0.24
ndh 2102401 c.642T>C synonymous_variant 0.38
ndh 2102407 c.636T>C synonymous_variant 0.13
ndh 2102739 p.Glu102* stop_gained 0.14
PPE35 2167965 p.Ala883Gly missense_variant 0.12
PPE35 2167967 c.2646A>C synonymous_variant 0.12
PPE35 2169269 c.1344A>G synonymous_variant 0.11
PPE35 2169272 c.1341C>A synonymous_variant 0.11
PPE35 2169278 c.1335T>C synonymous_variant 0.11
PPE35 2169281 c.1332T>G synonymous_variant 0.11
PPE35 2169789 p.Leu275* stop_gained 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.17
PPE35 2169910 p.Asn235Tyr missense_variant 0.16
PPE35 2169974 c.639T>C synonymous_variant 0.11
PPE35 2170400 c.213G>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.97
folC 2746999 p.Asp200Glu missense_variant 0.11
thyA 3074346 c.126C>T synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4039031 c.1674T>C synonymous_variant 0.1
clpC1 4039178 c.1527G>C synonymous_variant 0.11
clpC1 4040024 c.681A>G synonymous_variant 0.11
clpC1 4040027 c.678C>G synonymous_variant 0.11
clpC1 4040032 p.Val225Ile missense_variant 0.11
embC 4240801 c.939C>T synonymous_variant 0.12
embC 4240803 p.Tyr314Phe missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242660 p.Leu933Gln missense_variant 0.15
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4246285 p.Ser1018Leu missense_variant 0.11
embB 4247470 c.957T>C synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0