TB-Profiler result

Run: ERR144612
Summary

Run ID: ERR144612

Sample name:

Date: 31-03-2023 14:08:04

Number of reads: 6854082

Percentage reads mapped: 99.61

Strain: lineage4.8;lineage4.3.4.1;lineage4.1.2

Drug-resistance: RR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.48
lineage4.1 Euro-American T;X;H None 0.24
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.31
lineage4.1.2 Euro-American T;H None 0.06
lineage4.3.4 Euro-American (LAM) LAM RD174 0.48
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.47
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.His445Asn missense_variant 0.26 rifampicin
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 0.66
gyrA 9304 p.Gly668Asp missense_variant 0.75
mshA 575679 p.Asn111Ser missense_variant 0.13
rpoC 763783 c.414G>A synonymous_variant 0.49
rpoC 764995 c.1626C>G synonymous_variant 0.48
rpoC 765150 p.Gly594Glu missense_variant 0.19
rpoC 765325 c.1956C>T synonymous_variant 0.45
rpoC 765435 p.His689Arg missense_variant 0.15
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 1472954 n.1109T>C non_coding_transcript_exon_variant 0.1
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168147 p.Pro822Ser missense_variant 0.49
Rv1979c 2223123 c.42G>A synonymous_variant 0.46
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746540 c.1059G>A synonymous_variant 0.47
folC 2747263 c.336C>A synonymous_variant 0.19
ribD 2987307 p.Ala157Pro missense_variant 0.21
thyX 3067487 p.Lys153Asn missense_variant 0.5
thyA 3073806 c.666C>G synonymous_variant 0.28
thyA 3073868 p.Thr202Ala missense_variant 0.47
ald 3086788 c.-32T>C upstream_gene_variant 0.78
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.72
Rv3236c 3612009 p.Ala370Thr missense_variant 0.45
fbiB 3642576 p.Val348Ile missense_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 0.57
clpC1 4038857 c.1848C>A synonymous_variant 0.26
clpC1 4039729 p.Asp326Asn missense_variant 0.28
embC 4242425 p.Arg855Gly missense_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.2
embB 4249408 c.2895G>A synonymous_variant 0.16
ethR 4326910 c.-639G>A upstream_gene_variant 0.14
whiB6 4338550 c.-29A>T upstream_gene_variant 0.49
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.42