TB-Profiler result

Run: SRR6397579

Summary

Run ID: SRR6397579

Sample name:

Date: 19-10-2023 11:17:09

Number of reads: 5679076

Percentage reads mapped: 95.22

Strain: lineage4.4.1.2

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>A (0.13)
Amikacin R rrs n.1402C>A (0.13)
Capreomycin R rrs n.1402C>A (0.13)
Kanamycin R rrs n.1402C>A (0.13)
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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.2 Euro-American T1 None 0.99
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>A non_coding_transcript_exon_variant 0.13 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 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779565 c.-660G>C upstream_gene_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471658 n.-188T>C upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.14
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.15
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.14
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.15
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.14
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.15
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.25
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.22
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.19
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.2
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.19
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.18
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.19
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.18
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.19
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.11
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.11
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.11
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.12
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.13
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.13
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.12
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.14
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.11
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.11
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.12
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.11
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.12
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.12
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.12
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.12
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.12
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.12
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.11
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.12
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.12
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.12
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.12
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.12
rrl 1474799 n.1143delT non_coding_transcript_exon_variant 0.13
rrl 1474803 n.1146_1147insA non_coding_transcript_exon_variant 0.13
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.14
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.14
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.14
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.14
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.15
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.14
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.14
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.14
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.14
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.14
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.12
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.12
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.12
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.12
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.1
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.11
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.11
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.11
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.13
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.12
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.12
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 1476374 n.2717T>G non_coding_transcript_exon_variant 0.12
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.13
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.14
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2153960 p.Pro718Ser missense_variant 1.0
PPE35 2167770 p.Ser948Ile missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860213 p.Pro69Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249012 c.2499G>A synonymous_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0