TB-Profiler result

Run: ERR1035354
Summary

Run ID: ERR1035354

Sample name:

Date: 31-03-2023 10:12:35

Number of reads: 8119320

Percentage reads mapped: 99.13

Strain: lineage4.1.1

Drug-resistance: MDR-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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.99
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
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
katG 2155167 p.Ser315Arg missense_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 0.94
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776230 c.2251T>C synonymous_variant 0.98
rpsL 781370 c.-190G>C upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.14
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.12
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.11
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.14
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.15
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.13
rrl 1473924 n.267_268insT non_coding_transcript_exon_variant 0.12
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.17
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.16
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.16
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.15
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.15
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.15
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.15
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.18
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.11
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.14
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.16
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102769 p.Ile92Val missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.35
PPE35 2169866 c.747G>C synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073802 p.Pro224Ser missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878552 c.-45C>T upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.13
embC 4240195 c.333G>A synonymous_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0