TB-Profiler result

Run: SRR9971353
Summary

Run ID: SRR9971353

Sample name:

Date: 04-04-2023 23:24:37

Number of reads: 5482694

Percentage reads mapped: 98.76

Strain: lineage2.2.2

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289202 p.Cys14Arg missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4248002 p.Gln497Lys missense_variant 1.0 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide
gid 4407967 p.Leu79Ser missense_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
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
mshA 576108 p.Ala254Gly missense_variant 0.21
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.1
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.15
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.16
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.11
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.12
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.12
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.29
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.29
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.29
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.29
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.43
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.43
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.43
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.43
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.43
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.38
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.38
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.38
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.38
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.38
rrl 1476299 n.2642C>G non_coding_transcript_exon_variant 0.38
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.43
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.43
rrl 1476308 n.2651G>C non_coding_transcript_exon_variant 0.5
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.5
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.5
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.29
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.43
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.29
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.5
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.5
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.5
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.5
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.5
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.67
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.67
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.25
rrl 1476748 n.3091A>G non_coding_transcript_exon_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.98
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G 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
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0