TB-Profiler result

Run: ERR4815933
Summary

Run ID: ERR4815933

Sample name:

Date: 01-04-2023 14:08:47

Number of reads: 561373

Percentage reads mapped: 96.82

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
pncA 2288745 c.496delG frameshift_variant 0.11 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 760629 p.Leu275Met missense_variant 0.4
rpoB 760729 p.Tyr308Cys missense_variant 0.33
rpoC 766189 c.2822delG frameshift_variant 0.12
rpoC 766683 p.Val1105Ala missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800670 c.-139C>T upstream_gene_variant 0.25
rplC 801092 p.Tyr95Cys missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.67
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.67
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.67
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.67
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.75
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.6
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.71
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.67
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.67
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.67
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.67
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.67
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.67
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.67
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.67
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.67
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.5
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.5
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.5
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.4
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.67
fabG1 1673527 p.Ala30Ser missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101946 p.Asp366Gly missense_variant 0.2
ndh 2102664 c.378dupC frameshift_variant 0.5
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169768 p.Ala282Gly missense_variant 0.22
PPE35 2170282 p.Ala111Thr missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289147 p.Ser32Asn missense_variant 0.12
Rv2752c 3066204 c.-13G>T upstream_gene_variant 0.17
thyX 3067845 p.Ala34Val missense_variant 0.14
thyX 3067963 c.-18G>A upstream_gene_variant 0.22
thyA 3074438 p.Leu12Ile missense_variant 0.14
ald 3087298 c.482dupG frameshift_variant 0.12
fbiD 3339583 p.Thr156Ala missense_variant 0.12
Rv3083 3448322 c.-182G>A upstream_gene_variant 1.0
fprA 3474434 p.Pro143Leu missense_variant 0.15
fbiB 3642101 c.567C>A synonymous_variant 0.12
clpC1 4040313 p.Leu131Gln missense_variant 0.2
clpC1 4040565 p.Lys47Arg missense_variant 0.29
embC 4240301 p.Val147Met missense_variant 0.11
embC 4240344 p.Ala161Asp missense_variant 0.12
embA 4242643 c.-590C>T 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