TB-Profiler result

Run: SRR6650283
Summary

Run ID: SRR6650283

Sample name:

Date: 15-08-2023 07:59:00

Number of reads: 631049

Percentage reads mapped: 99.58

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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
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 0.25
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 0.25
fgd1 491027 p.Asn82Thr missense_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576723 p.Val459Gly missense_variant 0.38
ccsA 620532 c.642T>G synonymous_variant 0.2
ccsA 620537 p.Val216Gly missense_variant 0.23
ccsA 620551 p.Asp221His missense_variant 0.18
ccsA 620558 p.Gln223Pro missense_variant 0.17
ccsA 620561 p.Thr224Asn missense_variant 0.15
ccsA 620582 p.Arg231Pro missense_variant 0.13
ccsA 620752 p.Arg288Gly missense_variant 0.19
ccsA 620756 p.Asp289Gly missense_variant 0.24
ccsA 620805 c.915C>T synonymous_variant 0.17
rpoB 759615 c.-192A>C upstream_gene_variant 0.2
rpoB 759620 c.-187A>C upstream_gene_variant 0.18
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
rpoC 766914 p.Asp1182Ala missense_variant 0.21
mmpL5 775603 p.Thr960Pro missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776278 c.2201_2202dupGC frameshift_variant 0.22
mmpL5 777427 p.Thr352Pro missense_variant 0.25
mmpL5 778252 p.His77Asn missense_variant 0.18
mmpR5 779275 p.Arg96Trp missense_variant 1.0
mmpR5 779348 p.Val120Gly missense_variant 0.35
mmpR5 779363 p.Leu125Arg missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.39
atpE 1461086 c.42A>G synonymous_variant 0.25
atpE 1461119 c.75T>G synonymous_variant 0.38
atpE 1461131 c.87T>G synonymous_variant 0.22
atpE 1461140 c.96T>G synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673690 p.Val84Gly missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917986 p.Leu16Arg missense_variant 0.2
tlyA 1917989 p.Ala17Gly missense_variant 0.18
tlyA 1918014 p.Glu25Asp missense_variant 0.18
tlyA 1918044 p.Asp35Glu missense_variant 0.18
tlyA 1918052 p.Pro38Arg missense_variant 0.17
tlyA 1918055 p.Ala39Gly missense_variant 0.17
tlyA 1918059 c.120C>A synonymous_variant 0.17
tlyA 1918066 p.Ala43Pro missense_variant 0.25
ndh 2102777 p.Val89Gly missense_variant 0.14
ndh 2103225 c.-183A>C upstream_gene_variant 0.45
ndh 2103227 c.-185T>C upstream_gene_variant 0.2
ndh 2103235 c.-193C>G upstream_gene_variant 0.36
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167681 p.Ser978Pro missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169299 p.Asn438Lys missense_variant 0.33
PPE35 2169848 p.Asn255Lys missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.23
kasA 2518161 p.Val16Gly missense_variant 0.17
eis 2714569 p.Ala255Gly missense_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726263 p.Ser24Phe missense_variant 0.2
ahpC 2726269 p.Val26Gly missense_variant 0.3
ahpC 2726286 p.Gly32Arg missense_variant 0.33
ribD 2987312 c.474C>G synonymous_variant 0.25
ribD 2987314 p.Leu159Pro missense_variant 0.25
ribD 2987316 p.Ala160Pro missense_variant 0.25
ribD 2987320 p.Glu161Gly missense_variant 0.22
ribD 2987323 p.Val162Gly missense_variant 0.33
thyA 3074628 c.-157G>C upstream_gene_variant 0.2
thyA 3074633 c.-162C>G upstream_gene_variant 0.22
thyA 3074641 c.-170C>T upstream_gene_variant 0.38
thyA 3074645 c.-174T>G upstream_gene_variant 0.38
thyA 3074648 c.-177T>G upstream_gene_variant 0.33
thyA 3074654 c.-183T>G upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339608 p.Pro164Arg missense_variant 0.18
fbiD 3339616 p.Ser167Pro missense_variant 0.3
fbiD 3339626 p.His170Pro missense_variant 0.18
fprA 3473820 c.-187C>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841506 c.-86A>C upstream_gene_variant 0.3
clpC1 4039471 p.Ile412Val missense_variant 0.18
embC 4239973 c.111T>G synonymous_variant 0.29
embC 4240009 c.147G>A synonymous_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242393 p.Asp844Ala missense_variant 0.17
embA 4242406 c.-827A>C upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242908 p.Phe1016Val missense_variant 0.23
embA 4242952 c.-281T>G upstream_gene_variant 0.17
embA 4243350 p.Thr40Pro missense_variant 0.2
embB 4245581 c.-933C>A upstream_gene_variant 1.0
ubiA 4269833 c.1A>G start_lost 0.27
ubiA 4269848 c.-15A>G upstream_gene_variant 0.17
ethA 4326905 p.Leu190Pro missense_variant 0.2
ethR 4326907 c.-642C>G upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0