TB-Profiler result

Run: SRR1172090
Summary

Run ID: SRR1172090

Sample name:

Date: 03-04-2023 02:55:56

Number of reads: 1360879

Percentage reads mapped: 87.34

Strain: lineage4.4.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_variant 1.0 isoniazid, ethionamide
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
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 6144 p.His302Arg missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 766485 p.Val1039Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val 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 1472708 n.863T>A non_coding_transcript_exon_variant 0.11
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.15
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.16
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.15
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.16
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.14
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.11
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.11
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.13
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.14
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.14
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.14
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.14
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.14
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.14
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.14
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.15
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.16
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.16
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.26
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.22
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.18
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.17
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.19
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.21
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.21
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.26
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.23
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.15
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.14
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.15
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.14
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2156117 c.-6A>G upstream_gene_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288937 p.Ala102Val missense_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 0.97
ald 3086635 c.-185_-184insA upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3642749 c.1215T>C synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0