TB-Profiler result

Run: SRR6650220
Summary

Run ID: SRR6650220

Sample name:

Date: 15-08-2023 07:36:24

Number of reads: 1241537

Percentage reads mapped: 99.63

Strain: lineage3

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 R embB p.Leu359Ile (0.14)
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
lineage3 East-African-Indian CAS RD750 0.98
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
embB 4247588 p.Leu359Ile missense_variant 0.14 ethambutol
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 6913 p.Asn558Lys missense_variant 0.21
gyrB 6917 p.His560Phe missense_variant 0.13
gyrA 6922 c.-380G>T upstream_gene_variant 0.15
gyrB 6929 p.Ala564Pro missense_variant 0.21
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 491014 p.Thr78Pro missense_variant 0.42
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575165 c.-183C>T upstream_gene_variant 0.24
ccsA 619707 c.-184T>G upstream_gene_variant 0.25
ccsA 619709 c.-182T>G upstream_gene_variant 0.24
ccsA 619738 c.-153T>G upstream_gene_variant 0.21
ccsA 620546 p.Leu219Arg missense_variant 0.12
ccsA 620551 p.Asp221His missense_variant 0.16
ccsA 620748 c.858T>G synonymous_variant 0.5
ccsA 620752 p.Arg288Gly missense_variant 0.35
ccsA 620756 p.Asp289Gly missense_variant 0.4
ccsA 620761 p.Lys291Gln missense_variant 0.14
ccsA 620773 p.Ile295Val missense_variant 0.25
rpoB 759615 c.-192A>C upstream_gene_variant 0.3
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.18
atpE 1461101 c.57T>G synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474469 n.812T>G non_coding_transcript_exon_variant 0.25
fabG1 1673690 p.Val84Gly missense_variant 0.3
fabG1 1674076 p.Thr213Pro missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917989 p.Ala17Gly missense_variant 0.18
tlyA 1918031 p.Lys31Arg missense_variant 0.14
tlyA 1918040 p.Ile34Thr missense_variant 0.17
tlyA 1918044 p.Asp35Glu missense_variant 0.2
tlyA 1918049 p.Leu37Arg missense_variant 0.2
ndh 2102536 c.507G>A synonymous_variant 0.14
ndh 2102540 p.Ala168Gly missense_variant 0.23
ndh 2103225 c.-183A>C upstream_gene_variant 0.36
ndh 2103235 c.-193C>G upstream_gene_variant 0.41
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169317 c.1296C>T synonymous_variant 0.33
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.95
kasA 2518147 c.33C>T synonymous_variant 0.26
kasA 2518151 p.Ser13Arg missense_variant 0.21
kasA 2518161 p.Val16Gly missense_variant 0.18
eis 2715103 p.Leu77Pro missense_variant 0.19
ahpC 2726105 c.-88G>A upstream_gene_variant 0.96
ahpC 2726267 c.75G>A synonymous_variant 0.27
ahpC 2726269 p.Val26Gly missense_variant 0.38
ahpC 2726277 p.Lys29Gln missense_variant 0.17
ahpC 2726338 p.Val49Gly missense_variant 0.15
ahpC 2726341 p.Val50Gly missense_variant 0.21
ahpC 2726345 c.153C>T synonymous_variant 0.19
ahpC 2726350 p.Trp53Leu missense_variant 0.2
pepQ 2859438 c.981T>G synonymous_variant 0.19
ribD 2987314 p.Leu159Pro missense_variant 0.17
ribD 2987316 p.Ala160Pro missense_variant 0.16
ribD 2987323 p.Val162Gly missense_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.2
Rv3083 3448757 p.Ile85Thr missense_variant 0.19
Rv3083 3448765 p.Thr88Pro missense_variant 0.23
Rv3083 3449095 p.Gly198Arg missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612835 c.282T>G synonymous_variant 0.2
fbiB 3642877 p.Lys448Arg missense_variant 1.0
alr 3841506 c.-86A>C upstream_gene_variant 0.21
embC 4239973 c.111T>G synonymous_variant 0.38
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242414 p.Leu851Arg missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243350 p.Thr40Pro missense_variant 0.26
embB 4247621 c.1108C>T synonymous_variant 0.19
embB 4249293 p.Lys927Arg missense_variant 0.17
embB 4249305 p.Asn931Thr missense_variant 0.25
embB 4249323 p.Ala937Glu missense_variant 0.3
ubiA 4269502 p.Val111Gly missense_variant 0.2
aftB 4269504 c.-668A>G upstream_gene_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0