TB-Profiler result

Run: ERR036249
Summary

Run ID: ERR036249

Sample name:

Date: 31-03-2023 08:31:57

Number of reads: 5835371

Percentage reads mapped: 99.49

Strain: 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
lineage4.1 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 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.99
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.26
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406622 p.Leu240Arg missense_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.2
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.23
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169356 c.1257C>T synonymous_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2715586 c.-254G>C upstream_gene_variant 0.43
ahpC 2725954 c.-239C>T upstream_gene_variant 0.3
pepQ 2859381 c.1038C>G synonymous_variant 0.27
ribD 2987307 p.Ala157Pro missense_variant 0.18
Rv2752c 3064552 p.Arg547Pro missense_variant 0.24
thyA 3073806 c.666C>G synonymous_variant 0.21
thyA 3074654 c.-183T>G upstream_gene_variant 0.32
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fbiD 3339550 p.Gly145Trp missense_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.28
clpC1 4038857 c.1848C>A synonymous_variant 0.17
clpC1 4039932 p.Gly258Val missense_variant 0.21
embC 4239842 c.-21C>A upstream_gene_variant 0.28
embC 4242476 p.Pro872Ala missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.39
embC 4242827 p.Leu989Val missense_variant 0.22
ubiA 4269529 p.Ala102Gly missense_variant 0.26
ethA 4327346 p.Gly43Val missense_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0