TB-Profiler result

Run: ERR245835
Summary

Run ID: ERR245835

Sample name:

Date: 31-03-2023 18:23:49

Number of reads: 10746811

Percentage reads mapped: 99.74

Strain: lineage4.9.1

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
lineage4.9.1 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
ethA 4327054 p.Tyr140* stop_gained 0.18 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 8445 p.Arg382Gly missense_variant 0.27
gyrA 8978 c.1677C>T synonymous_variant 1.0
ccsA 620407 p.Pro173Ala missense_variant 0.2
rpoC 762836 c.-534C>G upstream_gene_variant 0.32
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417501 c.-154A>C upstream_gene_variant 0.29
atpE 1461019 c.-26C>A upstream_gene_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.25
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.24
inhA 1674892 p.Asn231Asp missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.46
Rv1979c 2223145 p.Arg7Lys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289138 p.Leu35Arg missense_variant 1.0
pncA 2289448 c.-207G>A upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.25
eis 2715586 c.-254G>C upstream_gene_variant 0.71
ahpC 2725954 c.-239C>T upstream_gene_variant 0.3
ahpC 2726756 c.564C>G synonymous_variant 0.24
folC 2746186 c.1413G>C synonymous_variant 0.24
Rv2752c 3064741 p.Gly484Ala missense_variant 0.22
Rv2752c 3067191 c.-1000G>A upstream_gene_variant 0.99
thyA 3073806 c.666C>G synonymous_variant 0.2
fbiD 3339385 p.Asp90Asn missense_variant 1.0
Rv3083 3449058 p.Ser185Arg missense_variant 0.3
Rv3083 3449673 p.Tyr390* stop_gained 0.24
fbiB 3641955 p.Gly141Arg missense_variant 0.3
ddn 3987013 p.Gly57Ala missense_variant 0.22
clpC1 4038857 c.1848C>A synonymous_variant 0.21
clpC1 4039363 p.Ala448Pro missense_variant 0.33
clpC1 4039932 p.Gly258Val missense_variant 0.23
embC 4241056 c.1194C>G synonymous_variant 0.2
embC 4241128 c.1266G>C synonymous_variant 0.23
embC 4241429 p.Phe523Val missense_variant 0.59
embC 4241456 p.Ala532Pro missense_variant 0.47
embC 4242425 p.Arg855Gly missense_variant 0.28
embC 4242476 p.Pro872Ala missense_variant 0.18
embC 4242822 p.Val987Gly missense_variant 0.4
embB 4249504 p.Gln997His missense_variant 0.21
ubiA 4269529 p.Ala102Gly missense_variant 0.16
ethA 4327672 c.-199G>A upstream_gene_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0