TB-Profiler result

Run: ERR4814834
Summary

Run ID: ERR4814834

Sample name:

Date: 01-04-2023 13:31:08

Number of reads: 1332941

Percentage reads mapped: 98.34

Strain: lineage3

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
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
pncA 2288691 c.550delT frameshift_variant 0.17 pyrazinamide
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 8714 p.Lys471Asn missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.28
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760865 c.1059C>T synonymous_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764181 p.Asp271Gly missense_variant 1.0
rpoC 766162 c.2793C>T synonymous_variant 0.11
rpoC 766960 c.3591C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779099 p.Gly37Asp missense_variant 0.11
mmpR5 779108 p.Leu40Ser missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407515 c.-175G>T upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471908 n.63A>G non_coding_transcript_exon_variant 0.1
rrs 1472882 n.1037A>G non_coding_transcript_exon_variant 1.0
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.5
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.5
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.5
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.5
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.5
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.5
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.33
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.33
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.67
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.5
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.33
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.33
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.33
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.33
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.5
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.5
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.5
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.5
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.5
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476267 n.2610G>T non_coding_transcript_exon_variant 0.5
rrl 1476276 n.2619C>A non_coding_transcript_exon_variant 0.67
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.67
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.67
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 1.0
rrl 1476295 n.2638C>A non_coding_transcript_exon_variant 1.0
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 1.0
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 1.0
rrl 1476306 n.2649A>G non_coding_transcript_exon_variant 1.0
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 1.0
rrl 1476311 n.2654G>T non_coding_transcript_exon_variant 1.0
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 1.0
rrl 1476599 n.2942C>T non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918359 c.420A>G synonymous_variant 0.1
ndh 2102382 c.661C>T synonymous_variant 0.11
ndh 2102389 c.654G>C synonymous_variant 0.11
ndh 2102411 p.Val211Gly missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155706 p.Pro136Ser missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170528 p.Ser29Ala missense_variant 0.11
PPE35 2170769 c.-157C>T 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
eis 2714938 p.Gly132Glu missense_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746614 p.Gly329Ser missense_variant 0.12
ribD 2987353 p.Thr172Met missense_variant 0.17
Rv2752c 3065517 c.674delT frameshift_variant 0.11
thyX 3067536 p.Asp137Ala missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474944 p.Leu313Pro missense_variant 0.12
fprA 3475000 p.Leu332Met missense_variant 0.13
fbiB 3641999 c.465C>A synonymous_variant 0.13
clpC1 4038164 c.2541G>C synonymous_variant 0.12
embC 4241654 p.Gly598Arg missense_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244204 p.Met324Ile missense_variant 0.11
embA 4245596 c.2367delA frameshift_variant 0.12
embB 4249010 p.Leu833Met missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408003 p.Asp67Ala missense_variant 1.0