TB-Profiler result

Run: SRR023453
Summary

Run ID: SRR023453

Sample name:

Date: 02-04-2023 14:11:46

Number of reads: 7634501

Percentage reads mapped: 92.18

Strain: lineage4.1.2.1

Drug-resistance: Sensitive

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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 0.99
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.32
fgd1 491014 p.Thr78Pro missense_variant 0.32
fgd1 491324 p.Val181Gly missense_variant 0.26
fgd1 491591 p.Lys270Met missense_variant 0.98
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 759816 p.Ser4Pro missense_variant 0.19
rpoB 759831 p.Thr9Pro missense_variant 0.29
rpoB 760115 c.309C>T synonymous_variant 0.97
rpoC 765150 p.Gly594Glu missense_variant 0.92
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777028 p.Thr485Pro missense_variant 0.26
mmpL5 777502 p.Thr327Pro missense_variant 0.27
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918058 p.Val40Gly missense_variant 0.21
katG 2154685 p.Ala476Val missense_variant 0.33
katG 2155726 p.Phe129Ser missense_variant 0.74
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.98
eis 2715098 p.Thr79Pro missense_variant 0.19
ahpC 2726338 p.Val49Gly missense_variant 0.27
ahpC 2726341 p.Val50Gly missense_variant 0.28
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474986 p.Val327Gly missense_variant 0.37
fbiB 3642049 p.Val172Gly missense_variant 0.19
embC 4240461 p.Val200Gly missense_variant 0.25
embC 4240646 p.Phe262Val missense_variant 0.33
embC 4241429 p.Phe523Val missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243963 p.Val244Gly missense_variant 0.31
embA 4244002 p.Val257Gly missense_variant 0.22
embA 4244217 p.Thr329Pro missense_variant 0.22
embA 4244641 p.Val470Gly missense_variant 0.31
embA 4244905 p.Val558Gly missense_variant 0.24
embB 4248614 p.Ala701Thr missense_variant 1.0
ubiA 4269317 p.Ser173Ala missense_variant 0.58