TB-Profiler result

Run: ERR4812495
Summary

Run ID: ERR4812495

Sample name:

Date: 20-10-2023 05:19:21

Number of reads: 3859929

Percentage reads mapped: 94.75

Strain: lineage4.1.2.1

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.799C>T (0.19)
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 1472644 n.799C>T non_coding_transcript_exon_variant 0.19 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417043 p.Arg102Pro missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472279 n.434T>C non_coding_transcript_exon_variant 0.1
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 0.1
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.17
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.18
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.18
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.16
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.16
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.16
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.15
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.2
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.15
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.15
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.1
rrs 1472840 n.995A>C non_coding_transcript_exon_variant 0.1
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.14
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 1473145 n.1300C>T non_coding_transcript_exon_variant 0.12
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.1
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.11
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.14
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.21
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.21
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.19
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.2
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.22
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.23
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.21
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.21
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.21
rrl 1475788 n.2131C>G non_coding_transcript_exon_variant 0.1
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.19
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.17
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.18
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.17
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.16
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.14
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.11
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.12
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.14
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.14
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.14
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.11
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.11
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.13
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.14
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.12
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.12
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.14
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.2
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.2
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.19
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.16
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.16
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.15
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.15
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.14
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.14
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T 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
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0