TB-Profiler result

Run: ERR6865989
Summary

Run ID: ERR6865989

Sample name:

Date: 02-04-2023 03:11:55

Number of reads: 1922351

Percentage reads mapped: 99.63

Strain: lineage4.3.3;lineage4.1.2.1

Drug-resistance: HR-TB

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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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.38
lineage4.1 Euro-American T;X;H None 0.63
lineage4.1.2 Euro-American T;H None 0.58
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.39
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.61
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
katG 2155168 p.Ser315Thr missense_variant 0.39 isoniazid
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 8040 p.Gly247Ser missense_variant 0.34
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.53
mshA 575679 p.Asn111Ser missense_variant 0.55
rpoB 759776 c.-31T>G upstream_gene_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 0.58
rpoC 764995 c.1626C>G synonymous_variant 0.41
rpoC 765150 p.Gly594Glu missense_variant 0.56
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.69
kasA 2518919 p.Gly269Ser missense_variant 0.41
thyA 3073868 p.Thr202Ala missense_variant 0.47
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339040 c.-78T>C upstream_gene_variant 0.62
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640393 c.-150A>C upstream_gene_variant 0.72
clpC1 4038287 c.2418C>T synonymous_variant 0.38
embC 4242182 p.Ala774Ser missense_variant 0.37
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.65
embB 4248043 c.1530C>G synonymous_variant 0.54
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407973 p.Val77Gly missense_variant 0.37
gid 4408156 p.Leu16Arg missense_variant 0.31
gid 4408312 c.-110C>T upstream_gene_variant 0.61