TB-Profiler result

Run: SRR5818591
Summary

Run ID: SRR5818591

Sample name:

Date: 21-10-2023 05:05:12

Number of reads: 3989468

Percentage reads mapped: 91.86

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 R rrs n.888G>A (0.18)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
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 0.99
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 1472733 n.888G>A non_coding_transcript_exon_variant 0.18 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 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 1472517 n.672T>A non_coding_transcript_exon_variant 0.15
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.15
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.22
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.22
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.25
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.24
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.25
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.28
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.24
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.21
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.27
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.27
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.23
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.31
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.25
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.21
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.19
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.11
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.11
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.11
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.13
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.16
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.16
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.19
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.16
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.12
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.1
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.14
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.19
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.21
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.2
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.22
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.23
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.29
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.31
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.28
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.36
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.38
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.38
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.14
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.32
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.39
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.39
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.21
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.3
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19
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