TB-Profiler result

Run: ERR2851355
Summary

Run ID: ERR2851355

Sample name:

Date: 31-03-2023 23:52:38

Number of reads: 115278

Percentage reads mapped: 66.68

Strain: lineage3

Drug-resistance: MDR-TB

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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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
gid 4407816 c.386delG frameshift_variant 1.0 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 5769 p.Pro177His missense_variant 0.2
gyrB 6824 p.Leu529Met missense_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8414 c.1113C>T synonymous_variant 1.0
gyrA 9119 c.1818A>G synonymous_variant 0.4
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9719 c.2418G>T synonymous_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761906 c.2100C>G synonymous_variant 0.25
rpoB 761934 p.Gly710Ser missense_variant 0.22
rpoB 762041 p.His745Gln missense_variant 0.29
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 764345 p.Pro326Thr missense_variant 0.18
rpoC 764817 p.Val483Ala missense_variant 1.0
rpoC 765583 c.2214G>T synonymous_variant 0.5
rpoC 765868 c.2499G>T synonymous_variant 0.67
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777076 p.Ala469Thr missense_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304156 p.Arg409Leu missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471981 n.136C>A non_coding_transcript_exon_variant 0.25
rrs 1472134 n.289C>A non_coding_transcript_exon_variant 0.17
rrs 1472247 n.402C>A non_coding_transcript_exon_variant 0.12
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.29
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.29
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.33
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.25
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.22
rrs 1472657 n.812G>T non_coding_transcript_exon_variant 0.25
rrl 1475278 n.1621G>T non_coding_transcript_exon_variant 0.25
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 1.0
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 1.0
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 1.0
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 1.0
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 1.0
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 1.0
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.67
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.67
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.67
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.67
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.67
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.5
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.75
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.75
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.75
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.67
rrl 1476299 n.2642C>G non_coding_transcript_exon_variant 0.4
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.4
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.6
rrl 1476308 n.2651G>C non_coding_transcript_exon_variant 0.29
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.71
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.71
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.43
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.25
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.25
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.38
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.33
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.43
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.43
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.33
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.33
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.29
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.43
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.43
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.33
inhA 1674510 p.Met103Ile missense_variant 0.67
rpsA 1833563 p.Ser8Pro missense_variant 0.5
rpsA 1834456 c.915T>A synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2221839 c.1326T>C synonymous_variant 0.25
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
kasA 2517957 c.-158G>T upstream_gene_variant 0.15
kasA 2518531 c.417G>T synonymous_variant 0.25
eis 2714605 p.Ala243Glu missense_variant 0.5
ahpC 2726103 c.-90G>A upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2860602 c.-184A>G upstream_gene_variant 0.29
thyA 3074620 c.-149C>A upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087808 p.Arg330Leu missense_variant 0.5
Rv3083 3449000 p.Pro166Gln missense_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840602 c.819G>T synonymous_variant 0.4
embC 4240142 c.280C>T synonymous_variant 1.0
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241355 p.Gln498Arg missense_variant 0.4
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244213 c.981C>A synonymous_variant 1.0
embB 4249591 c.3078C>T synonymous_variant 0.67
embB 4249779 p.Trp1089Leu missense_variant 0.33
ethA 4326036 p.Phe480Ile missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407666 c.537C>A synonymous_variant 0.18