TB-Profiler result

Run: ERR4822198

Summary

Run ID: ERR4822198

Sample name:

Date: 01-04-2023 17:41:27

Number of reads: 253426

Percentage reads mapped: 89.22

Strain: lineage4

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
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.88 streptomycin
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
gyrB 6431 p.Ala398Thr missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575331 c.-17C>A upstream_gene_variant 0.67
mshA 575856 p.Ala170Glu missense_variant 0.18
rpoB 761233 p.Arg476Pro missense_variant 0.4
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777772 p.Val237Leu missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407286 p.Ala19Thr missense_variant 0.25
embR 1416734 c.613delG frameshift_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
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 0.5
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.5
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 0.71
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.67
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.67
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.67
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.88
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.9
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.91
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.82
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.67
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.67
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 1.0
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 1.0
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.67
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.67
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.29
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.22
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154495 c.1617C>A synonymous_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223325 c.-161G>A upstream_gene_variant 0.33
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2715435 c.-104_-103insG upstream_gene_variant 0.29
ahpC 2725991 c.-202C>T upstream_gene_variant 0.5
Rv2752c 3067135 c.-944C>T upstream_gene_variant 1.0
thyX 3067510 c.436C>T synonymous_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339098 c.-20G>A upstream_gene_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640546 p.Lys2Glu missense_variant 0.22
fbiB 3640593 c.-942C>T upstream_gene_variant 0.5
fbiB 3642808 p.Ala425Val missense_variant 0.33
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247198 p.Thr229Ser missense_variant 0.33
ethA 4327131 p.Arg115Ser missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407720 c.483C>G synonymous_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.83