TB-Profiler result

Run: ERR3994109
Summary

Run ID: ERR3994109

Sample name:

Date: 01-04-2023 03:42:41

Number of reads: 1886276

Percentage reads mapped: 99.97

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
katG 2155341 p.Met257Ile missense_variant 0.18 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
ccsA 620700 c.810C>T synonymous_variant 0.11
rpoB 760527 p.Gln241* stop_gained 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302871 c.-60C>T upstream_gene_variant 0.29
fbiC 1303769 c.840delG frameshift_variant 0.11
Rv1258c 1406376 p.Gly322Asp missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.12
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.12
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.12
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.16
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.44
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.52
rrs 1472184 n.339T>C non_coding_transcript_exon_variant 0.33
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.47
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154353 c.1759C>T synonymous_variant 0.11
katG 2156384 c.-273G>A upstream_gene_variant 1.0
PPE35 2169031 p.Asp528Asn missense_variant 0.18
PPE35 2169041 c.1572G>A synonymous_variant 0.29
PPE35 2169044 c.1569G>C synonymous_variant 0.6
PPE35 2169047 p.Ile522Val missense_variant 0.5
PPE35 2169053 c.1560T>C synonymous_variant 1.0
PPE35 2169056 c.1557A>G synonymous_variant 0.5
PPE35 2169059 c.1554G>A synonymous_variant 0.5
PPE35 2169063 p.Met517Thr missense_variant 1.0
PPE35 2169065 p.Ala516Ile missense_variant 0.5
PPE35 2169068 c.1545G>T synonymous_variant 0.5
PPE35 2169071 c.1542A>G synonymous_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859596 p.Ala275Thr missense_variant 0.17
fbiB 3642539 c.1005G>A synonymous_variant 0.14
alr 3840764 c.657G>C synonymous_variant 1.0
alr 3840850 p.Arg191Trp missense_variant 0.12
clpC1 4038967 p.Ile580Val missense_variant 0.11
clpC1 4040295 p.Gln137Arg missense_variant 0.1
clpC1 4040830 c.-126G>A upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245958 p.Gly909Val missense_variant 0.2
embA 4246327 p.Phe1032Ser missense_variant 0.11
embB 4246859 p.Val116Ile missense_variant 0.15
embB 4248937 p.Gln808His missense_variant 0.14
aftB 4267715 c.1122G>A synonymous_variant 0.12
aftB 4268368 p.Cys157Ser missense_variant 0.12
aftB 4268418 c.418delG frameshift_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0