TB-Profiler result

Run: SRR5341254

Summary

Run ID: SRR5341254

Sample name:

Date: 21-10-2023 01:26:54

Number of reads: 2444723

Percentage reads mapped: 90.72

Strain: lineage4.2.2.2

Drug-resistance: Other


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1402C>T (1.00)
Amikacin R rrs n.1402C>T (1.00)
Capreomycin R rrs n.1402C>T (1.00)
Kanamycin R rrs n.1402C>T (1.00)
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR 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
rrs 1473247 n.1402C>T non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
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 8630 c.1329G>A synonymous_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 761489 c.1683G>A synonymous_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 1472616 n.771G>A non_coding_transcript_exon_variant 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.12
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.21
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.21
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.2
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.2
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.2
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.2
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.21
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.19
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.21
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.19
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.19
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.19
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.19
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.18
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.18
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.19
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.15
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.16
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.2
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.38
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.41
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.44
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.37
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.37
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.37
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.37
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.37
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.34
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.38
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.4
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.4
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.4
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.52
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.58
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.6
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.6
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.56
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.56
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.52
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.52
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.51
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.52
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.5
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.44
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.37
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.29
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.24
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.24
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.23
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.23
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.23
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.23
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.23
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.23
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.23
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C 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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0