TB-Profiler result

Run: SRR6982172
Summary

Run ID: SRR6982172

Sample name:

Date: 04-04-2023 18:29:34

Number of reads: 562921

Percentage reads mapped: 99.58

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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
ethA 4326030 c.1443delC frameshift_variant 0.11 ethionamide
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777050 c.1431G>A synonymous_variant 0.11
mmpL5 777300 p.Leu394Pro missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304748 c.1821delC frameshift_variant 0.11
Rv1258c 1406791 p.Ser184Thr missense_variant 0.12
embR 1417472 c.-125A>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673560 p.Lys41Leu missense_variant 0.11
rpsA 1833388 c.-154C>T upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2155742 p.Gly124Cys missense_variant 0.12
PPE35 2169019 c.1593dupG frameshift_variant 0.13
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2222341 p.Met275Thr missense_variant 1.0
Rv1979c 2222356 p.Thr270Ile missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3641010 c.-525C>T upstream_gene_variant 1.0
rpoA 3878044 p.Ser155* stop_gained 0.11
clpC1 4039020 p.Leu562Pro missense_variant 0.1
panD 4044104 p.Ile60Val missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245512 c.2280G>C synonymous_variant 1.0
embA 4245735 p.Ala835Ser missense_variant 0.17
embA 4245943 p.Arg904His missense_variant 0.11
embB 4246775 p.Val88Leu missense_variant 0.11
embB 4249294 p.Lys927Asn missense_variant 0.15
embB 4249526 p.Gly1005Ser missense_variant 0.12
aftB 4268740 p.Ile33Val missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0