TB-Profiler result

Run: SRR6650117
Summary

Run ID: SRR6650117

Sample name:

Date: 15-08-2023 07:57:37

Number of reads: 2082874

Percentage reads mapped: 99.82

Strain: lineage4.4.1.2

Drug-resistance: Sensitive

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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
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
lineage4.4 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 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
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 6325 c.-977C>G upstream_gene_variant 0.83
gyrB 6894 p.Met552Arg missense_variant 0.17
gyrB 6913 p.Asn558Lys missense_variant 0.18
gyrB 6918 p.His560Leu missense_variant 0.17
gyrA 6922 c.-380G>T upstream_gene_variant 0.17
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 490751 c.-32T>G upstream_gene_variant 0.29
fgd1 490756 c.-27T>G upstream_gene_variant 0.29
fgd1 490759 c.-24A>T upstream_gene_variant 0.29
fgd1 490761 c.-22G>T upstream_gene_variant 0.14
fgd1 490763 c.-20C>G upstream_gene_variant 0.17
fgd1 490771 c.-12T>G upstream_gene_variant 0.21
fgd1 490780 c.-3C>A upstream_gene_variant 0.2
fgd1 490784 p.Val1Gly missense_variant 0.18
fgd1 490787 p.Ala2Gly missense_variant 0.18
fgd1 491014 p.Thr78Pro missense_variant 0.24
fgd1 491027 p.Asn82Thr missense_variant 0.19
ccsA 619831 c.-60T>G upstream_gene_variant 0.18
ccsA 620551 p.Asp221His missense_variant 0.14
ccsA 620748 c.858T>G synonymous_variant 0.24
ccsA 620752 p.Arg288Gly missense_variant 0.22
ccsA 620756 p.Asp289Gly missense_variant 0.22
ccsA 620773 p.Ile295Val missense_variant 0.17
rpoB 759611 c.-196G>C upstream_gene_variant 0.27
rpoB 759615 c.-192A>C upstream_gene_variant 0.27
rpoB 759618 c.-189T>C upstream_gene_variant 0.18
rpoB 759620 c.-187A>C upstream_gene_variant 0.17
rpoC 763897 c.528G>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778002 p.Ser160* stop_gained 1.0
mmpR5 779348 p.Val120Gly missense_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.22
atpE 1461086 c.42A>G synonymous_variant 0.3
atpE 1461101 c.57T>G synonymous_variant 0.22
atpE 1461119 c.75T>G synonymous_variant 0.25
atpE 1461125 c.81T>G synonymous_variant 0.23
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473945 n.288T>G non_coding_transcript_exon_variant 0.22
rrl 1473953 n.296T>G non_coding_transcript_exon_variant 0.22
rrl 1473959 n.302T>G non_coding_transcript_exon_variant 0.25
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.22
rrl 1474500 n.843T>G non_coding_transcript_exon_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.41
ndh 2103227 c.-185T>C upstream_gene_variant 0.21
ndh 2103235 c.-193C>G upstream_gene_variant 0.29
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
kasA 2518147 c.33C>T synonymous_variant 0.28
kasA 2518151 p.Ser13Arg missense_variant 0.21
kasA 2518161 p.Val16Gly missense_variant 0.22
eis 2715103 p.Leu77Pro missense_variant 0.24
ahpC 2726269 p.Val26Gly missense_variant 0.21
ahpC 2726338 p.Val49Gly missense_variant 0.25
ahpC 2726341 p.Val50Gly missense_variant 0.24
ahpC 2726345 c.153C>T synonymous_variant 0.17
ahpC 2726350 p.Trp53Leu missense_variant 0.22
ahpC 2726360 p.Asp56Glu missense_variant 0.15
pepQ 2860213 p.Pro69Leu missense_variant 1.0
ribD 2987314 p.Leu159Pro missense_variant 0.14
ribD 2987316 p.Ala160Pro missense_variant 0.17
ribD 2987320 p.Glu161Gly missense_variant 0.19
ribD 2987323 p.Val162Gly missense_variant 0.31
thyA 3074641 c.-170C>T upstream_gene_variant 0.21
thyA 3074645 c.-174T>G upstream_gene_variant 0.21
thyA 3074648 c.-177T>G upstream_gene_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.24
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611988 p.Leu377Val missense_variant 0.18
clpC1 4039484 c.1221T>G synonymous_variant 0.29
embC 4239973 c.111T>G synonymous_variant 0.17
embC 4240655 p.Ala265Pro missense_variant 0.27
embC 4240661 p.Trp267Arg missense_variant 0.15
embC 4242220 c.2358A>C synonymous_variant 0.36
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245250 p.His673Arg missense_variant 1.0
embB 4247616 p.Glu368Gly missense_variant 0.16
embB 4247623 c.1110G>C synonymous_variant 0.19
embB 4249012 c.2499G>A synonymous_variant 1.0
embB 4249298 p.Trp929Gly missense_variant 0.15
embB 4249305 p.Asn931Thr missense_variant 0.18
embB 4249323 p.Ala937Glu missense_variant 0.26
embB 4249329 p.Met939Arg missense_variant 0.12
aftB 4268776 p.Ser21Gly missense_variant 0.24
ubiA 4269502 p.Val111Gly missense_variant 0.17
aftB 4269504 c.-668A>G upstream_gene_variant 0.23
ubiA 4269511 p.Val108Gly missense_variant 0.17
ubiA 4269848 c.-15A>G upstream_gene_variant 0.21
ethA 4327519 c.-46C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0