TB-Profiler result

Run: ERR1199064
Summary

Run ID: ERR1199064

Sample name:

Date: 14-08-2022 01:41:38

Number of reads: 10838336

Percentage reads mapped: 94.11

Strain: lineage4.6.1.1

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
lineage4.6 Euro-American T;LAM None 0.99
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.99
lineage4.6.1.1 Euro-American T2-Uganda RD724 0.99
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.14 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 0.95
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575930 p.Glu195* stop_gained 0.15
rpoC 762836 c.-534C>G upstream_gene_variant 0.36
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416222 p.Phe376Leu missense_variant 0.13
embR 1416232 p.Cys372Gly missense_variant 0.15
embR 1416259 c.1089G>C synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.13
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.17
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.17
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.17
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.17
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.18
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.17
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.23
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.18
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.14
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.16
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.15
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.23
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.11
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.16
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.16
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.19
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.15
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.29
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.29
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.29
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.22
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.19
clpC1 4039363 p.Ala448Pro missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.33
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0