TB-Profiler result

Run: SRR6650399
Summary

Run ID: SRR6650399

Sample name:

Date: 15-08-2023 08:23:50

Number of reads: 1166647

Percentage reads mapped: 99.55

Strain: lineage4.1.2.1

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
lineage4.1.2 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
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
gyrB 6918 p.His560Leu missense_variant 0.2
gyrA 6922 c.-380G>T upstream_gene_variant 0.18
gyrB 6934 p.Gln565His missense_variant 0.18
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 490979 p.Asn66Thr missense_variant 0.31
fgd1 491014 p.Thr78Pro missense_variant 0.23
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575176 c.-172T>G upstream_gene_variant 0.16
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575886 p.Leu180Arg missense_variant 0.17
ccsA 619777 c.-114C>G upstream_gene_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.25
ccsA 619879 c.-12A>G upstream_gene_variant 0.18
ccsA 619896 p.Asn2Lys missense_variant 0.15
ccsA 620551 p.Asp221His missense_variant 0.19
ccsA 620578 p.Tyr230His missense_variant 0.12
ccsA 620748 c.858T>G synonymous_variant 0.26
ccsA 620756 p.Asp289Gly missense_variant 0.24
ccsA 620763 c.873G>A synonymous_variant 0.14
ccsA 620770 p.Trp294Arg missense_variant 0.14
ccsA 620773 p.Ile295Val missense_variant 0.19
ccsA 620778 p.Asn296Lys missense_variant 0.2
rpoB 759615 c.-192A>C upstream_gene_variant 0.22
rpoB 759620 c.-187A>C upstream_gene_variant 0.16
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775595 c.2886C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.26
Rv1258c 1407069 p.Leu91Pro missense_variant 0.18
atpE 1461101 c.57T>G synonymous_variant 0.31
atpE 1461108 p.Ile22Leu missense_variant 0.13
atpE 1461119 c.75T>G synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473856 n.199A>C non_coding_transcript_exon_variant 0.27
fabG1 1674076 p.Thr213Pro missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918015 p.Leu26Val missense_variant 0.2
tlyA 1918031 p.Lys31Arg missense_variant 0.18
tlyA 1918052 p.Pro38Arg missense_variant 0.18
tlyA 1918061 p.Lys41Arg missense_variant 0.2
ndh 2102502 p.Thr181Pro missense_variant 0.14
ndh 2102538 p.Lys169Gln missense_variant 0.19
ndh 2102540 p.Ala168Gly missense_variant 0.25
ndh 2103225 c.-183A>C upstream_gene_variant 0.3
ndh 2103235 c.-193C>G upstream_gene_variant 0.32
PPE35 2170018 p.Ala199Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289500 c.-259A>G upstream_gene_variant 0.21
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.28
kasA 2518151 p.Ser13Arg missense_variant 0.17
kasA 2518605 p.Val164Gly missense_variant 0.24
eis 2714566 p.Leu256Pro missense_variant 0.21
ahpC 2726338 p.Val49Gly missense_variant 0.16
ahpC 2726341 p.Val50Gly missense_variant 0.29
ahpC 2726345 c.153C>T synonymous_variant 0.18
ahpC 2726350 p.Trp53Leu missense_variant 0.3
ahpC 2726355 p.Lys55Glu missense_variant 0.16
ahpC 2726360 p.Asp56Glu missense_variant 0.14
thyA 3074641 c.-170C>T upstream_gene_variant 0.16
thyA 3074648 c.-177T>G upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448705 p.Pro68Ser missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 0.13
Rv3236c 3612800 p.Val106Gly missense_variant 0.18
clpC1 4038163 p.Arg848Gly missense_variant 0.17
embC 4239973 c.111T>G synonymous_variant 0.16
embC 4242225 p.Asn788Thr missense_variant 0.14
embA 4242406 c.-827A>C upstream_gene_variant 0.29
embC 4242414 p.Leu851Arg missense_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243350 p.Thr40Pro missense_variant 0.21
embA 4243365 p.Trp45Gly missense_variant 0.17
embA 4244619 p.Leu463Val missense_variant 0.19
embA 4244905 p.Val558Gly missense_variant 0.21
embA 4244911 p.Leu560Pro missense_variant 0.15
embA 4244928 p.Thr566Pro missense_variant 0.14
embB 4249305 p.Asn931Thr missense_variant 0.17
embB 4249323 p.Ala937Glu missense_variant 0.23
aftB 4268776 p.Ser21Gly missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0