TB-Profiler result

Run: ERR4816940

Summary

Run ID: ERR4816940

Sample name:

Date: 01-04-2023 14:43:03

Number of reads: 1142026

Percentage reads mapped: 97.78

Strain: lineage3.1.2

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 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 0.43 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.43
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.43
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.43
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.38
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.38
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.36
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.4
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.36
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.36
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.2
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.22
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.22
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.22
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.43
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.43
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.38
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.38
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.43
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.43
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.14
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.14
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.15
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.15
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.14
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.14
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.13
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.19
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.12
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.22
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.22
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.25
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.22
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.22
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.22
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.22
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.22
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.22
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.2
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.21
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.2
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.14
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918696 p.Ala253Pro missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.29
PPE35 2169910 p.Asn235Tyr missense_variant 0.26
PPE35 2170147 p.Ser156Ala missense_variant 0.19
Rv1979c 2223257 c.-93G>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2290173 c.-932C>T upstream_gene_variant 0.2
eis 2715432 c.-100C>T upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475052 p.Asn349Thr missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244351 c.1119G>A synonymous_variant 0.12
embB 4248241 c.1728C>G synonymous_variant 1.0
aftB 4268654 c.183A>G synonymous_variant 0.15
ethR 4327693 p.Asp49Asn missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408147 p.Ala19Val missense_variant 1.0