TB-Profiler result

Run: ERR4818634
Summary

Run ID: ERR4818634

Sample name:

Date: 01-04-2023 15:40:05

Number of reads: 417123

Percentage reads mapped: 91.31

Strain: lineage4.6.1

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
lineage4.6.1 Euro-American (Uganda) T2 RD724 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.8 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 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7699 p.Arg133Gln missense_variant 0.14
gyrA 7709 c.408G>A synonymous_variant 1.0
gyrA 8003 c.702C>T synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.23
mshA 575887 c.540G>A synonymous_variant 0.25
mshA 575890 c.543C>T synonymous_variant 0.25
rpoC 764379 p.Thr337Lys missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777156 p.Arg442Gln missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781770 p.Gly71Ser missense_variant 0.17
Rv1258c 1407095 c.246G>A synonymous_variant 0.12
embR 1417538 c.-191A>T upstream_gene_variant 0.25
atpE 1460888 c.-157C>T upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472427 n.582T>A non_coding_transcript_exon_variant 1.0
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.5
rrs 1472471 n.626G>A non_coding_transcript_exon_variant 0.5
rrs 1472484 n.639A>T non_coding_transcript_exon_variant 0.5
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.5
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.67
rrs 1472504 n.659A>T non_coding_transcript_exon_variant 0.5
rrs 1472505 n.660G>A non_coding_transcript_exon_variant 0.4
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.4
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.4
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.4
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 1.0
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 1.0
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 1.0
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 1.0
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 1.0
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.86
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 1.0
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 1.0
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 1.0
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.86
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.88
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.88
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.78
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.78
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.67
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 1.0
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 1.0
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.75
rrl 1476657 n.3000G>A non_coding_transcript_exon_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167910 c.2703C>T synonymous_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289967 c.-726C>T upstream_gene_variant 0.11
kasA 2519219 p.Pro369Ser missense_variant 0.18
ahpC 2726338 p.Val49Gly missense_variant 0.33
ald 3086675 c.-145A>G upstream_gene_variant 0.11
Rv3083 3449723 p.Cys407Tyr missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641549 c.15A>G synonymous_variant 0.17
alr 3840291 p.Gln377Leu missense_variant 0.11
alr 3840890 c.531C>T synonymous_variant 0.11
panD 4044191 p.Asp31Asn missense_variant 0.14
embC 4242034 c.2172C>A synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 0.94
embA 4244163 p.Leu311Ile missense_variant 0.15
embA 4245038 p.Asn602Lys missense_variant 0.14
embB 4248317 p.Val602Pro missense_variant 0.11
embB 4248320 p.Gly603Thr missense_variant 0.11
aftB 4268015 c.822G>T synonymous_variant 0.17
aftB 4268375 p.Met154Ile missense_variant 0.29
aftB 4268519 c.318C>T synonymous_variant 1.0
ubiA 4269217 p.Ile206Thr missense_variant 0.18
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338529 c.-8T>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407742 p.Arg154Gln missense_variant 1.0