TB-Profiler result

Run: SRR7765063
Summary

Run ID: SRR7765063

Sample name:

Date: 04-04-2023 20:19:17

Number of reads: 1733551

Percentage reads mapped: 93.84

Strain: lineage4.8

Drug-resistance: Pre-XDR-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
gyrA 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.5 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4326840 c.633delC frameshift_variant 1.0 ethionamide
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
rpoC 765804 p.Thr812Ile missense_variant 1.0
rpoC 766466 p.Glu1033Lys missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.13
mmpL5 777122 c.1359C>T synonymous_variant 0.13
mmpL5 777128 c.1353A>G synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.75
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.4
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.5
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.6
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.67
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.75
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.5
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.43
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.43
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.33
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.67
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.5
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.5
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.67
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.67
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.67
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.67
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.5
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.33
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.67
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.5
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.5
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.5
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.75
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.67
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.75
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.25
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.5
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.36
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.36
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.45
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.3
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.33
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.2
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.22
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.5
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.3
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.22
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.22
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.22
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.22
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.56
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.22
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.78
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.75
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.5
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.67
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.75
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.75
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.75
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.75
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.75
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.33
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.33
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.22
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.22
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155010 p.Phe368Leu missense_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.22
PPE35 2170053 p.Thr187Ser missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289808 c.-567C>T upstream_gene_variant 1.0
ald 3086796 c.-24C>T upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408064 p.Arg47Trp missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0