TB-Profiler result

Run: ERR2229717

Summary

Run ID: ERR2229717

Sample name:

Date: 31-03-2023 17:28:55

Number of reads: 444162

Percentage reads mapped: 99.46

Strain: lineage4

Drug-resistance: Sensitive


Download CSV Download TXT Download PDF Download JSON
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
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
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 9326 c.2025G>T synonymous_variant 0.13
mshA 576765 p.Thr473Met missense_variant 0.5
rpoB 760168 p.Met121Thr missense_variant 0.29
rpoB 760861 p.Pro352Leu missense_variant 0.14
rpoC 763629 p.Val87Ala missense_variant 0.11
rpoC 765918 p.Phe850Ser missense_variant 0.23
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775726 c.2755C>T synonymous_variant 0.12
mmpL5 775727 c.2754C>G synonymous_variant 0.12
mmpL5 775736 c.2745C>G synonymous_variant 0.13
mmpL5 775741 c.2740C>T synonymous_variant 0.12
mmpL5 775742 c.2739C>T synonymous_variant 0.11
mmpL5 775747 p.Met912Leu missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781808 c.249C>A synonymous_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416671 p.Gly226Ala missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.39
rpsA 1833392 c.-150C>A upstream_gene_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156520 c.-409G>A upstream_gene_variant 0.14
PPE35 2167965 p.Ala883Gly missense_variant 0.14
PPE35 2167967 c.2646A>C synonymous_variant 0.14
PPE35 2167997 c.2616G>C synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169109 p.Asp502Asn missense_variant 0.12
PPE35 2169269 c.1344A>G synonymous_variant 0.18
PPE35 2169272 c.1341C>G synonymous_variant 0.18
PPE35 2169725 c.888T>C synonymous_variant 0.13
PPE35 2169840 p.Gly258Asp missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.83
PPE35 2170053 p.Thr187Ser missense_variant 0.88
Rv1979c 2223182 c.-18C>A upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067703 p.Tyr81* stop_gained 0.29
fbiD 3339372 c.255C>A synonymous_variant 0.25
fbiA 3640405 c.-138G>T upstream_gene_variant 0.12
fbiB 3642630 p.Thr366Ser missense_variant 0.17
rpoA 3877539 p.Tyr323* stop_gained 0.25
clpC1 4038579 p.Phe709Tyr missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243422 p.Ser64Pro missense_variant 0.2
embA 4246285 p.Ser1018Leu missense_variant 0.2
embB 4246544 p.Thr11Pro missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407731 p.Arg158* stop_gained 0.22
gid 4408273 c.-71C>G upstream_gene_variant 0.2
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0