TB-Profiler result

Run: ERR1274707
Summary

Run ID: ERR1274707

Sample name:

Date: 31-03-2023 13:30:33

Number of reads: 790537

Percentage reads mapped: 90.14

Strain: lineage4.1.1

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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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
inhA 1674048 c.-154G>A 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760493 c.687C>A synonymous_variant 1.0
rpoB 761147 c.1341C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765719 p.Glu784Gln missense_variant 1.0
rpoC 766070 c.2701C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776203 p.Gly760Cys missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303789 p.Ile287Val missense_variant 0.17
embR 1416954 p.Glu132Lys missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472352 n.507T>C non_coding_transcript_exon_variant 0.15
rrs 1472999 n.1154C>T non_coding_transcript_exon_variant 0.12
rrl 1473832 n.175C>A non_coding_transcript_exon_variant 0.12
rrl 1474132 n.475G>A non_coding_transcript_exon_variant 0.14
rrl 1475439 n.1782A>G non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154579 c.1533C>T synonymous_variant 0.11
PPE35 2169939 p.Gly225Ala missense_variant 0.14
PPE35 2169941 c.672C>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987030 c.195delC frameshift_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641447 p.Thr302Met missense_variant 1.0
fbiB 3642248 p.Asn238Lys missense_variant 0.12
rpoA 3877553 p.Glu319Lys missense_variant 1.0
clpC1 4040241 p.Thr155Phe missense_variant 0.18
clpC1 4040249 p.Glu152Gly missense_variant 0.18
embC 4240897 c.1035C>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.11
embB 4246548 p.Pro12Gln missense_variant 0.1
embB 4246555 c.42G>C synonymous_variant 0.19
embB 4246556 p.Ala15Pro missense_variant 0.19
embB 4246563 p.Leu17Trp missense_variant 0.19
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0