TB-Profiler result

Run: ERR2652955
Summary

Run ID: ERR2652955

Sample name:

Date: 31-03-2023 22:25:06

Number of reads: 1069743

Percentage reads mapped: 99.73

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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
pncA 2288883 p.Leu120Pro missense_variant 0.14 pyrazinamide
ethR 4327831 p.Ala95Thr missense_variant 0.11 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 7396 p.Ala32Val missense_variant 0.13
mshA 576093 c.749delG frameshift_variant 0.14
mshA 576618 p.His424Arg missense_variant 0.12
ccsA 619805 c.-86C>T upstream_gene_variant 0.13
rpoB 761145 p.Arg447Cys missense_variant 0.12
rpoB 762657 p.Ala951Thr missense_variant 0.14
rpoC 763187 c.-183C>T upstream_gene_variant 0.13
rpoB 763254 p.Glu1150Gln missense_variant 0.12
rpoC 766994 p.Gly1209Cys missense_variant 0.18
mmpL5 775659 c.2821delC frameshift_variant 0.11
mmpL5 779079 c.-599C>T upstream_gene_variant 0.11
mmpS5 779612 c.-707G>A upstream_gene_variant 0.13
fbiC 1303643 p.Pro238Leu missense_variant 1.0
fbiC 1304865 c.1935C>T synonymous_variant 0.21
fbiC 1304939 p.Glu670Val missense_variant 0.13
embR 1417195 c.153A>G synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476719 n.3062C>T non_coding_transcript_exon_variant 0.15
rrl 1476744 n.3087G>T non_coding_transcript_exon_variant 0.17
tlyA 1917784 c.-156C>T upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918060 p.Lys41Glu missense_variant 0.1
tlyA 1918507 p.Gly190Ser missense_variant 0.1
ndh 2102714 c.328delA frameshift_variant 0.15
katG 2155377 c.735G>T synonymous_variant 0.11
katG 2155810 p.Leu101Pro missense_variant 0.11
PPE35 2168386 p.Glu743Lys missense_variant 0.11
PPE35 2170161 p.Met151Thr missense_variant 0.14
Rv1979c 2221740 c.1425C>T synonymous_variant 0.13
pncA 2289736 c.-495T>C upstream_gene_variant 0.17
kasA 2518589 p.Gly159Trp missense_variant 0.12
kasA 2519046 p.His311Arg missense_variant 0.17
kasA 2519124 p.Tyr337Cys missense_variant 0.17
eis 2715278 p.Leu19Val missense_variant 0.1
ahpC 2726113 c.-80A>T upstream_gene_variant 0.17
folC 2747746 c.-148A>C upstream_gene_variant 0.11
pepQ 2859836 p.Ala195Thr missense_variant 0.2
pepQ 2860477 c.-59A>C upstream_gene_variant 0.11
pepQ 2860573 c.-155A>G upstream_gene_variant 0.1
Rv2752c 3066265 c.-74A>T upstream_gene_variant 0.12
thyX 3067644 c.301delT frameshift_variant 0.11
Rv3236c 3612841 c.276G>A synonymous_variant 0.12
fbiA 3640417 c.-126C>T upstream_gene_variant 0.13
fbiA 3640811 p.Gln90Arg missense_variant 0.11
fbiB 3641151 c.-384G>A upstream_gene_variant 0.12
fbiB 3641362 c.-173C>A upstream_gene_variant 0.12
fbiB 3641861 c.327C>T synonymous_variant 0.17
fbiB 3641965 p.Val144Ala missense_variant 0.15
fbiB 3642844 p.Asp437Gly missense_variant 0.12
fbiB 3642874 p.Leu447Pro missense_variant 0.12
alr 3840489 p.Pro311Leu missense_variant 0.12
ddn 3986662 c.-182A>G upstream_gene_variant 0.11
clpC1 4038911 c.1794G>A synonymous_variant 0.14
embC 4240480 c.618G>A synonymous_variant 0.15
embC 4240860 p.Leu333Arg missense_variant 1.0
embA 4243632 p.Gly134Arg missense_variant 0.11
embA 4243935 p.Asp235Asn missense_variant 0.13
embA 4244325 p.Gly365Ser missense_variant 1.0
embA 4244729 c.1498_1499insCTGTC frameshift_variant 0.11
embB 4247096 p.Pro195Thr missense_variant 0.12
whiB6 4338300 c.222G>A synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0