TB-Profiler result

Run: ERR4820221
Summary

Run ID: ERR4820221

Sample name:

Date: 01-04-2023 16:33:23

Number of reads: 538692

Percentage reads mapped: 99.45

Strain: lineage4.8

Drug-resistance: Other

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
pncA 2288766 p.Leu159Pro missense_variant 0.17 pyrazinamide
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
rpoB 761336 p.Tyr510* stop_gained 0.33
rpoB 763068 p.Asp1088Asn missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778107 p.Ser125Cys missense_variant 1.0
mmpL5 778870 c.-390G>T upstream_gene_variant 0.15
mmpL5 778907 c.-427C>T upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476606 n.2949A>C non_coding_transcript_exon_variant 0.29
fabG1 1674076 p.Thr213Pro missense_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917984 c.45C>G synonymous_variant 0.67
katG 2155568 p.Gly182Trp missense_variant 0.17
PPE35 2167965 p.Ala883Gly missense_variant 0.25
PPE35 2167967 c.2646A>C synonymous_variant 0.25
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168206 p.Pro803Ala missense_variant 0.2
PPE35 2169668 c.945C>A synonymous_variant 0.5
PPE35 2170229 c.384A>G synonymous_variant 0.12
PPE35 2170232 c.381T>A synonymous_variant 0.12
PPE35 2170238 c.375T>G synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289505 c.-264G>T upstream_gene_variant 0.29
eis 2715297 c.36C>T synonymous_variant 0.25
folC 2747278 c.321C>A synonymous_variant 0.33
Rv2752c 3065492 p.Ile234Leu missense_variant 0.4
ald 3086891 c.72G>A synonymous_variant 0.11
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612135 p.Thr328Ala missense_variant 0.29
clpC1 4039437 p.Glu423Gly missense_variant 0.33
clpC1 4039484 c.1221T>G synonymous_variant 0.33
embA 4242337 c.-896C>A upstream_gene_variant 1.0
embC 4242894 p.Ile1011Asn missense_variant 0.25
embA 4245099 p.Gly623Trp missense_variant 0.2
ubiA 4269514 p.Val107Gly missense_variant 0.5
ethA 4328378 c.-905G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0