TB-Profiler result

Run: SRR6650379
Summary

Run ID: SRR6650379

Sample name:

Date: 15-08-2023 07:38:31

Number of reads: 761514

Percentage reads mapped: 99.7

Strain: lineage4.5

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
lineage4.5 Euro-American H;T RD122 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 1.0
gyrA 9157 p.Asp619Ala missense_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.43
fgd1 490756 c.-27T>G upstream_gene_variant 0.29
fgd1 490759 c.-24A>T upstream_gene_variant 0.43
fgd1 490771 c.-12T>G upstream_gene_variant 0.38
fgd1 490777 c.-6G>A upstream_gene_variant 0.22
fgd1 490780 c.-3C>A upstream_gene_variant 0.33
fgd1 490784 p.Val1Gly missense_variant 0.33
fgd1 490787 p.Ala2Gly missense_variant 0.3
fgd1 490979 p.Asn66Thr missense_variant 0.25
fgd1 491000 p.Ser73Trp missense_variant 0.14
fgd1 491008 p.Thr76Pro missense_variant 0.23
fgd1 491014 p.Thr78Pro missense_variant 0.36
fgd1 491027 p.Asn82Thr missense_variant 0.25
mshA 576723 p.Val459Gly missense_variant 0.33
ccsA 619730 c.-161A>C upstream_gene_variant 0.22
ccsA 619831 c.-60T>G upstream_gene_variant 0.3
ccsA 620029 c.139C>T synonymous_variant 1.0
ccsA 620532 c.642T>G synonymous_variant 0.36
ccsA 620752 p.Arg288Gly missense_variant 0.29
ccsA 620756 p.Asp289Gly missense_variant 0.25
ccsA 620773 p.Ile295Val missense_variant 0.18
ccsA 620797 p.Met303Leu missense_variant 0.19
rpoB 759611 c.-196G>C upstream_gene_variant 0.3
rpoB 759615 c.-192A>C upstream_gene_variant 0.3
rpoB 759620 c.-187A>C upstream_gene_variant 0.27
rpoC 766914 p.Asp1182Ala missense_variant 0.18
rpoC 766920 p.Ala1184Gly missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779353 c.-873G>A upstream_gene_variant 0.22
mmpR5 779363 p.Leu125Arg missense_variant 0.27
mmpL5 779367 c.-887G>C upstream_gene_variant 0.17
mmpR5 779371 p.Ala128Pro missense_variant 0.2
mmpS5 779490 c.-585T>G upstream_gene_variant 1.0
rpsL 781363 c.-197T>G upstream_gene_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.19
fbiC 1303016 p.Val29Gly missense_variant 0.18
fbiC 1303031 p.Arg34Pro missense_variant 0.14
Rv1258c 1406101 p.Pro414Ser missense_variant 1.0
atpE 1461083 c.39T>G synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 0.29
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.4
rrl 1474500 n.843T>G non_coding_transcript_exon_variant 0.5
rrl 1475075 n.1418A>C non_coding_transcript_exon_variant 0.25
rpsA 1834245 p.Val235Gly missense_variant 0.23
rpsA 1834256 p.Glu239Gln missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918061 p.Lys41Arg missense_variant 0.29
tlyA 1918066 p.Ala43Pro missense_variant 0.2
tlyA 1918069 p.Thr44Pro missense_variant 0.2
ndh 2103225 c.-183A>C upstream_gene_variant 0.22
ndh 2103235 c.-193C>G upstream_gene_variant 0.18
katG 2155667 p.Trp149Gly missense_variant 0.18
PPE35 2169293 c.1320T>G synonymous_variant 0.25
PPE35 2169299 p.Asn438Lys missense_variant 0.15
PPE35 2169317 c.1296C>T synonymous_variant 0.33
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726258 p.Asp22Glu missense_variant 0.13
ahpC 2726269 p.Val26Gly missense_variant 0.31
folC 2747688 c.-90G>C upstream_gene_variant 0.17
thyA 3074613 c.-142C>G upstream_gene_variant 0.18
thyA 3074641 c.-170C>T upstream_gene_variant 0.27
thyA 3074645 c.-174T>G upstream_gene_variant 0.25
thyA 3074648 c.-177T>G upstream_gene_variant 0.25
fbiD 3339273 c.156T>G synonymous_variant 0.42
fbiD 3339279 c.162T>G synonymous_variant 0.18
Rv3083 3449188 p.Val229Ile missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474423 p.Glu139Asp missense_variant 1.0
whiB7 3568411 p.Ala90Val missense_variant 0.14
fbiB 3642512 p.Leu326Phe missense_variant 0.15
fbiB 3642740 c.1206C>T synonymous_variant 0.25
fbiB 3642744 p.Ala404Ser missense_variant 0.25
fbiB 3642751 p.Asp406Gly missense_variant 0.22
fbiB 3642769 p.Leu412Arg missense_variant 0.25
clpC1 4038318 p.Pro796Leu missense_variant 1.0
clpC1 4040252 c.453C>G synonymous_variant 0.13
embC 4239973 c.111T>G synonymous_variant 0.21
embC 4240006 c.144A>C synonymous_variant 0.19
embC 4242220 c.2358A>C synonymous_variant 0.31
embC 4242225 p.Asn788Thr missense_variant 0.18
embA 4242406 c.-827A>C upstream_gene_variant 0.33
embC 4242422 p.Trp854Gly missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242950 p.Gly1030Arg missense_variant 0.15
embA 4242958 c.-275G>C upstream_gene_variant 0.25
embA 4242964 c.-269C>G upstream_gene_variant 0.17
embA 4243350 p.Thr40Pro missense_variant 0.21
embA 4244980 p.Val583Gly missense_variant 0.29
embB 4246711 p.Ser66Arg missense_variant 0.13
embB 4247597 p.Trp362Gly missense_variant 0.16
embB 4248711 p.Tyr733Cys missense_variant 0.14
embB 4249291 c.2778C>A synonymous_variant 0.2
embB 4249298 p.Trp929Gly missense_variant 0.33
embB 4249305 p.Asn931Thr missense_variant 0.5
embB 4249314 p.Phe934Ser missense_variant 0.29
embB 4249323 p.Ala937Glu missense_variant 0.67
aftB 4269486 c.-650T>G upstream_gene_variant 0.15
ubiA 4269833 c.1A>G start_lost 0.2
ethA 4326905 p.Leu190Pro missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0