TB-Profiler result

Run: SRR6650243
Summary

Run ID: SRR6650243

Sample name:

Date: 15-08-2023 07:36:55

Number of reads: 1988132

Percentage reads mapped: 99.54

Strain: lineage4.1.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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 6649 c.-653T>G upstream_gene_variant 0.16
gyrB 6913 p.Asn558Lys missense_variant 0.15
gyrA 6922 c.-380G>T upstream_gene_variant 0.19
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7695 p.Ala132Pro missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491008 p.Thr76Pro missense_variant 0.21
fgd1 491014 p.Thr78Pro missense_variant 0.27
fgd1 491027 p.Asn82Thr missense_variant 0.26
mshA 576723 p.Val459Gly missense_variant 0.19
ccsA 619831 c.-60T>G upstream_gene_variant 0.18
ccsA 620748 c.858T>G synonymous_variant 0.16
rpoB 759615 c.-192A>C upstream_gene_variant 0.17
rpoB 759620 c.-187A>C upstream_gene_variant 0.23
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
rplC 801287 p.Val160Gly missense_variant 0.29
atpE 1461086 c.42A>G synonymous_variant 0.24
atpE 1461119 c.75T>G synonymous_variant 0.24
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.25
rrl 1474500 n.843T>G non_coding_transcript_exon_variant 0.25
rrl 1475075 n.1418A>C non_coding_transcript_exon_variant 0.17
inhA 1673368 c.-834A>G upstream_gene_variant 1.0
fabG1 1673690 p.Val84Gly missense_variant 0.22
fabG1 1674076 p.Thr213Pro missense_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918044 p.Asp35Glu missense_variant 0.15
tlyA 1918059 c.120C>A synonymous_variant 0.21
ndh 2103235 c.-193C>G upstream_gene_variant 0.19
PPE35 2169293 c.1320T>G synonymous_variant 0.16
PPE35 2170082 c.531T>G synonymous_variant 0.24
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518161 p.Val16Gly missense_variant 0.15
eis 2714566 p.Leu256Pro missense_variant 0.29
ahpC 2726210 c.18T>C synonymous_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.16
ahpC 2726269 p.Val26Gly missense_variant 0.17
ahpC 2726277 p.Lys29Gln missense_variant 0.18
ahpC 2726338 p.Val49Gly missense_variant 0.24
ahpC 2726341 p.Val50Gly missense_variant 0.22
ahpC 2726345 c.153C>T synonymous_variant 0.22
ahpC 2726350 p.Trp53Leu missense_variant 0.24
ahpC 2726360 p.Asp56Glu missense_variant 0.16
ahpC 2726375 p.Cys61Trp missense_variant 0.15
ribD 2987316 p.Ala160Pro missense_variant 0.19
Rv2752c 3065602 p.Asp197Gly missense_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641447 p.Thr302Met missense_variant 1.0
fbiB 3642751 p.Asp406Ala missense_variant 0.17
rpoA 3877553 p.Glu319Lys missense_variant 1.0
clpC1 4039451 c.1254G>C synonymous_variant 0.17
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249323 p.Ala937Glu missense_variant 0.25
embB 4249408 c.2895G>A synonymous_variant 1.0
ethR 4327813 p.Thr89Pro missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0