TB-Profiler result

Run: ERR4815868
Summary

Run ID: ERR4815868

Sample name:

Date: 01-04-2023 14:06:36

Number of reads: 88409

Percentage reads mapped: 80.2

Strain: lineage4

Drug-resistance: RR-TB

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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
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
rpoB 761095 p.Leu430Pro missense_variant 1.0 rifampicin
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 7585 p.Ser95Thr missense_variant 1.0
fgd1 490833 c.51G>A synonymous_variant 0.4
rpoB 763113 p.Gly1103Cys missense_variant 0.4
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305150 c.2220C>A synonymous_variant 0.25
Rv1258c 1407357 c.-17A>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.17
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472342 n.497G>T non_coding_transcript_exon_variant 0.5
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.67
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.67
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.5
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 0.7
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.7
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.43
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.62
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.5
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.29
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.43
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.29
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.5
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 1.0
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.67
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.67
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.67
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.67
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.67
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.67
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.67
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.67
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.33
rrs 1473318 n.1473G>T non_coding_transcript_exon_variant 0.33
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.67
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.4
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.33
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.29
inhA 1673661 c.-541G>A upstream_gene_variant 1.0
inhA 1674248 p.Ile16Ser missense_variant 0.4
inhA 1674544 p.Asp115Tyr missense_variant 0.67
rpsA 1834012 c.471G>T synonymous_variant 0.5
rpsA 1834015 c.474G>C synonymous_variant 0.5
rpsA 1834024 c.483G>C synonymous_variant 0.5
rpsA 1834025 p.Gln162Ala missense_variant 0.5
rpsA 1834040 p.Lys167Gln missense_variant 0.67
rpsA 1834043 p.Glu168Gln missense_variant 0.67
rpsA 1834046 p.Ile169Leu missense_variant 0.67
rpsA 1834051 c.510G>A synonymous_variant 0.67
rpsA 1834054 c.513C>T synonymous_variant 0.67
rpsA 1834090 c.549G>T synonymous_variant 0.5
rpsA 1834093 c.552G>T synonymous_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918683 c.744C>T synonymous_variant 0.67
ndh 2102567 p.Glu159Ala missense_variant 1.0
katG 2155507 p.Ala202Asp missense_variant 1.0
PPE35 2169871 p.Gly248Ser missense_variant 0.5
ahpC 2726164 c.-29C>A upstream_gene_variant 0.4
ahpC 2726372 c.180G>T synonymous_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074657 c.-186C>G upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642663 p.Val377Ile missense_variant 0.5
clpC1 4038176 c.2529G>T synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040408 c.297C>A synonymous_variant 0.29
embC 4241766 p.Ala635Asp missense_variant 0.5
embC 4241807 p.Pro649Thr missense_variant 0.5
embA 4243705 p.Gly158Asp missense_variant 1.0
aftB 4269600 c.-764C>A upstream_gene_variant 0.33
ethA 4327034 p.Tyr147Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407869 p.Val112Phe missense_variant 0.67
gid 4408156 p.Leu16Arg missense_variant 1.0