TB-Profiler result

Run: SRR13180246
Summary

Run ID: SRR13180246

Sample name:

Date: 03-04-2023 08:15:14

Number of reads: 1931311

Percentage reads mapped: 91.15

Strain: lineage4.8

Drug-resistance: HR-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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
katG 2145477 c.-419_*8411del transcript_ablation 1.0 isoniazid
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 5758 p.Phe173Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407356 c.-16T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.13
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.11
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.11
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.14
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.11
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.11
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.11
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.12
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.12
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.15
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.13
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.14
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.13
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.15
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.16
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.15
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.13
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.13
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.16
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.29
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.16
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.13
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.14
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.26
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.24
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.27
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.16
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.2
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.14
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.24
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.26
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.14
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.16
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.16
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.18
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.18
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.11
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.19
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.19
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.2
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.2
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.2
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.26
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.24
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
rpoA 3878530 c.-23C>T upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0