TB-Profiler result

Run: ERR10796644
Summary

Run ID: ERR10796644

Sample name:

Date: 31-03-2023 11:13:06

Number of reads: 831474

Percentage reads mapped: 100.0

Strain: lineage4

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
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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
fgd1 490595 c.-188G>A upstream_gene_variant 0.14
fgd1 490756 c.-27T>G upstream_gene_variant 0.3
mshA 576446 p.Thr367Pro missense_variant 0.5
rpoB 759894 p.Pro30Ala missense_variant 0.18
rpoB 760270 p.Thr155Ile missense_variant 0.11
rpoB 763231 p.Arg1142His missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779277 c.-797C>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304881 p.Glu651Lys missense_variant 0.17
fbiC 1304901 c.1971C>T synonymous_variant 0.17
fbiC 1304934 c.2004C>T synonymous_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473252 n.1407T>A non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474114 n.457C>A non_coding_transcript_exon_variant 0.25
rrl 1474223 n.566A>G non_coding_transcript_exon_variant 0.5
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.14
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.14
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.14
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.14
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.15
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.15
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.15
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.22
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.13
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.15
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.17
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.17
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.17
rrl 1476371 n.2714A>G non_coding_transcript_exon_variant 0.17
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.17
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.18
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.18
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.18
rrl 1476393 n.2736C>T non_coding_transcript_exon_variant 0.36
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.25
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.57
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.4
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.33
rpsA 1833925 c.384C>A synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101665 p.Lys460Glu missense_variant 0.15
katG 2154517 p.Ala532Val missense_variant 0.12
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168211 p.Ile801Asn missense_variant 0.11
PPE35 2169791 p.Asn274Lys missense_variant 0.14
Rv1979c 2223081 c.84C>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289563 c.-322G>T upstream_gene_variant 0.14
kasA 2517982 c.-133G>A upstream_gene_variant 0.11
pepQ 2860021 p.Glu133Val missense_variant 0.15
Rv2752c 3064588 p.Arg535His missense_variant 0.15
Rv2752c 3065182 p.Ser337Leu missense_variant 1.0
thyX 3067826 c.120C>T synonymous_variant 0.22
thyA 3073915 p.His186Leu missense_variant 0.15
whiB7 3568617 c.63C>T synonymous_variant 1.0
embC 4240827 p.Ala322Val missense_variant 0.5
embC 4241465 p.Phe535Leu missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243830 p.Gly200Ser missense_variant 0.18
embA 4244667 p.Val479Met missense_variant 1.0
embA 4244874 p.Pro548Ser missense_variant 1.0
embB 4247917 c.1404C>A synonymous_variant 0.29
embB 4247992 c.1479G>A synonymous_variant 1.0
aftB 4269732 c.-896C>T upstream_gene_variant 0.17
ubiA 4269864 c.-31C>T upstream_gene_variant 1.0
ethA 4327519 c.-46C>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0