TB-Profiler result

Run: ERR245806
Summary

Run ID: ERR245806

Sample name:

Date: 31-03-2023 18:22:27

Number of reads: 9481884

Percentage reads mapped: 99.44

Strain: lineage4.8

Drug-resistance: Sensitive

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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
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 7493 c.192C>T synonymous_variant 0.24
mshA 575308 c.-40A>G upstream_gene_variant 0.25
ccsA 620407 p.Pro173Ala missense_variant 0.28
rpoB 759831 p.Thr9Pro missense_variant 0.27
rpoB 762249 p.Leu815Val missense_variant 0.18
rpoC 762836 c.-534C>G upstream_gene_variant 0.35
rpoC 764725 p.Phe452Leu missense_variant 0.23
rpoC 767305 p.Tyr1312* stop_gained 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.23
mmpL5 779181 c.-701G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800997 p.Asn63Lys missense_variant 0.18
atpE 1461019 c.-26C>A upstream_gene_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.19
rrl 1476408 n.2751G>C non_coding_transcript_exon_variant 0.23
fabG1 1673449 p.Thr4Pro missense_variant 0.41
inhA 1674892 p.Asn231Asp missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.23
PPE35 2168149 p.Pro822Ser missense_variant 0.99
PPE35 2169320 p.Leu431Phe missense_variant 0.23
PPE35 2169866 c.747G>C synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.2
eis 2714787 p.Trp182* stop_gained 1.0
eis 2715586 c.-254G>C upstream_gene_variant 0.65
ahpC 2725954 c.-239C>T upstream_gene_variant 0.29
folC 2746186 c.1413G>C synonymous_variant 0.21
Rv2752c 3064741 p.Gly484Ala missense_variant 0.21
ald 3086750 c.-70A>C upstream_gene_variant 1.0
ald 3086982 p.Ala55Pro missense_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.83
fprA 3474601 p.Arg199Gly missense_variant 0.28
fbiB 3641955 p.Gly141Arg missense_variant 0.18
fbiB 3642734 c.1200G>C synonymous_variant 0.14
ddn 3987013 p.Gly57Ala missense_variant 0.31
clpC1 4038857 c.1848C>A synonymous_variant 0.2
clpC1 4039363 p.Ala448Pro missense_variant 0.34
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4039932 p.Gly258Val missense_variant 0.24
embC 4241056 c.1194C>G synonymous_variant 0.32
embC 4241429 p.Phe523Val missense_variant 0.39
embC 4241456 p.Ala532Pro missense_variant 0.46
embC 4242425 p.Arg855Gly missense_variant 0.13
embC 4242476 p.Pro872Ala missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.52
embC 4242827 p.Leu989Val missense_variant 0.22
embB 4249504 p.Gln997His missense_variant 0.2
ethA 4327672 c.-199G>A upstream_gene_variant 0.38
ethR 4327912 p.Arg122Gly missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0