TB-Profiler result

Run: ERR4815211

Summary

Run ID: ERR4815211

Sample name:

Date: 01-04-2023 13:44:18

Number of reads: 1040746

Percentage reads mapped: 99.09

Strain: lineage4.1.2.1

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
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 0.99
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8534 c.1233G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9487 p.Gly729Val missense_variant 0.29
fgd1 491132 p.Gly117Ala missense_variant 0.13
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620012 p.Gly41Asp missense_variant 0.12
ccsA 620535 p.Met215Ile missense_variant 0.25
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760653 p.Lys283Glu missense_variant 0.1
rpoB 763140 p.Pro1112Ser missense_variant 0.14
rpoC 764479 p.Glu370Asp missense_variant 0.18
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765345 p.Gly659Ala missense_variant 0.22
rpoC 766404 p.Met1012Thr missense_variant 0.17
rpoC 767226 p.Pro1286Leu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777248 c.1233C>T synonymous_variant 0.11
mmpL5 777606 p.Gly292Val missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303329 c.399C>T synonymous_variant 1.0
fbiC 1305471 c.2541C>A synonymous_variant 0.33
Rv1258c 1406700 p.Glu214Ala missense_variant 0.19
embR 1417172 c.175delC frameshift_variant 0.15
embR 1417270 c.78C>A synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.4
rrs 1472230 n.385C>A non_coding_transcript_exon_variant 0.4
rrl 1476622 n.2965G>T non_coding_transcript_exon_variant 0.17
rpsA 1833874 c.333T>C synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155278 c.834C>T synonymous_variant 0.17
katG 2155664 p.Pro150Ser missense_variant 0.2
PPE35 2168296 p.Glu773* stop_gained 0.14
PPE35 2170066 p.Ala183Thr missense_variant 0.33
Rv1979c 2222821 p.Ser115Leu missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288950 p.Ala98Ser missense_variant 0.12
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518542 p.Gln143Pro missense_variant 0.25
kasA 2518940 p.His276Asp missense_variant 0.11
eis 2715303 p.Glu10Asp missense_variant 0.14
eis 2715309 c.23dupC frameshift_variant 0.15
folC 2746665 p.Phe312Leu missense_variant 0.12
folC 2747101 c.498G>T synonymous_variant 0.2
folC 2747740 c.-142A>G upstream_gene_variant 0.11
Rv2752c 3065307 p.Met295Ile missense_variant 0.17
Rv2752c 3065582 p.Thr204Ala missense_variant 0.15
Rv2752c 3067189 c.-998G>A upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087391 p.Gly191Asp missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640354 c.-189C>T upstream_gene_variant 1.0
fbiB 3642598 c.1065delC frameshift_variant 0.11
alr 3841592 c.-172A>G upstream_gene_variant 0.22
rpoA 3878203 p.Pro102Leu missense_variant 0.22
clpC1 4038400 p.Gly769Arg missense_variant 0.11
clpC1 4039071 p.Pro545Leu missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242890 p.Arg1010Gly missense_variant 0.18
embA 4244054 c.822C>T synonymous_variant 0.12
embA 4244218 p.Thr329Ile missense_variant 0.13
embA 4246059 p.Ala943Thr missense_variant 0.12
embB 4247700 p.Met396Thr missense_variant 0.11
aftB 4267329 p.Arg503Leu missense_variant 0.12
aftB 4267425 p.Gly471Glu missense_variant 0.12
aftB 4268611 p.Pro76Ser missense_variant 0.22
aftB 4268910 c.-74T>A upstream_gene_variant 0.4
ethA 4328404 c.-931T>C upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0