TB-Profiler result

Run: ERR4829907
Summary

Run ID: ERR4829907

Sample name:

Date: 01-04-2023 19:45:32

Number of reads: 2523157

Percentage reads mapped: 97.23

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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.4 streptomycin
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 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 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.12
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.25
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.14
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.15
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.15
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.22
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.25
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.29
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.29
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.25
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.29
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.29
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.29
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.29
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.33
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.33
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.33
rrs 1472583 n.738T>C non_coding_transcript_exon_variant 0.33
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.29
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.33
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.12
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.12
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.13
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.13
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.12
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.12
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.12
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.12
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 0.2
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.2
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.22
rrl 1474660 n.1003G>A non_coding_transcript_exon_variant 0.33
rrl 1474673 n.1016T>G non_coding_transcript_exon_variant 0.33
rrl 1474674 n.1017A>G non_coding_transcript_exon_variant 0.33
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.33
rrl 1474690 n.1033C>T non_coding_transcript_exon_variant 0.33
rrl 1474752 n.1096delA non_coding_transcript_exon_variant 0.38
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.33
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.3
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.3
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.3
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.22
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.22
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.22
rrl 1475094 n.1437C>T non_coding_transcript_exon_variant 0.29
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154325 p.Asn596Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840771 p.Ala217Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ethA 4328435 c.-962C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0