TB-Profiler result

Run: ERR2229577
Summary

Run ID: ERR2229577

Sample name:

Date: 10-04-2023 19:13:22

Number of reads: 894362

Percentage reads mapped: 99.14

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 5913 p.Asp225Gly missense_variant 0.11
gyrB 6438 p.Pro400Leu missense_variant 0.14
gyrB 6632 p.Gly465Ser missense_variant 0.2
gyrB 6687 p.Gly483Asp missense_variant 0.11
gyrB 7139 p.Arg634Ser missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8691 p.Asp464Asn missense_variant 0.12
gyrA 9299 c.1998G>A synonymous_variant 0.14
mshA 575271 c.-77C>A upstream_gene_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.38
mshA 576111 p.Ala255Gly missense_variant 0.2
ccsA 620460 c.570T>C synonymous_variant 0.12
rpoB 759950 c.144T>C synonymous_variant 0.17
rpoB 761572 p.Pro589His missense_variant 0.15
rpoC 765500 p.Gln711Lys missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776378 p.Phe701Leu missense_variant 0.2
mmpL5 776417 c.2064G>C synonymous_variant 0.18
mmpL5 777329 c.1152C>T synonymous_variant 0.33
mmpL5 777733 p.Leu250Val missense_variant 0.12
mmpR5 778190 c.-800G>C upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801142 p.Val112Ile missense_variant 0.21
fbiC 1303347 c.417T>A synonymous_variant 0.11
fbiC 1303502 p.Leu191Pro missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.35
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.32
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.15
rrl 1473922 n.265A>G non_coding_transcript_exon_variant 0.15
rrl 1473923 n.266C>G non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.22
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.22
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.22
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.15
rrl 1475145 n.1488C>T non_coding_transcript_exon_variant 0.17
rrl 1475163 n.1506T>G non_coding_transcript_exon_variant 0.17
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.13
rrl 1476315 n.2658C>A non_coding_transcript_exon_variant 0.15
rrl 1476319 n.2662C>A non_coding_transcript_exon_variant 0.17
rrl 1476577 n.2920T>C non_coding_transcript_exon_variant 0.14
fabG1 1673346 c.-94C>G upstream_gene_variant 0.24
fabG1 1673349 c.-91G>C upstream_gene_variant 0.24
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.44
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102648 p.Ala132Val missense_variant 0.12
PPE35 2167695 p.Ile973Thr missense_variant 0.14
PPE35 2167745 p.Thr956Arg missense_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169125 p.Val496Ile missense_variant 0.15
PPE35 2169902 p.Leu237Phe missense_variant 0.3
PPE35 2169910 p.Asn235Tyr missense_variant 0.26
PPE35 2170048 p.Leu189Val missense_variant 0.53
PPE35 2170053 p.Thr187Ser missense_variant 0.54
PPE35 2170147 p.Ser156Ala missense_variant 0.17
PPE35 2170157 p.Ala152Ser missense_variant 0.12
PPE35 2170392 p.Gly74Ala missense_variant 0.22
PPE35 2170400 c.213G>C synonymous_variant 0.23
Rv1979c 2222534 p.Ala211Thr missense_variant 0.15
Rv1979c 2223032 p.Pro45Ser missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290156 c.-915G>A upstream_gene_variant 0.29
kasA 2517936 c.-179G>A upstream_gene_variant 0.17
kasA 2518864 c.750G>C synonymous_variant 0.17
kasA 2518964 p.Gly284Cys missense_variant 0.12
folC 2747278 c.321C>A synonymous_variant 0.12
folC 2747780 c.-182C>A upstream_gene_variant 0.25
pepQ 2859643 p.Ala259Val missense_variant 0.18
ribD 2987588 p.Tyr250* stop_gained 0.12
Rv2752c 3064531 p.Thr554Met missense_variant 0.22
Rv2752c 3066203 c.-12G>T upstream_gene_variant 0.12
Rv2752c 3066391 c.-200C>T upstream_gene_variant 0.17
Rv3083 3448454 c.-50C>A upstream_gene_variant 0.13
fprA 3475071 c.1065C>T synonymous_variant 0.14
Rv3236c 3612623 p.Tyr165Phe missense_variant 0.2
Rv3236c 3613286 c.-170C>A upstream_gene_variant 0.12
fbiB 3641546 c.12C>T synonymous_variant 0.17
fbiB 3641628 p.Ala32Thr missense_variant 0.17
fbiB 3642292 p.Arg253His missense_variant 0.14
fbiB 3642295 p.Gln254Leu missense_variant 0.14
alr 3840575 c.846G>A synonymous_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.52
clpC1 4039325 p.Gln460His missense_variant 0.15
clpC1 4039526 c.1179G>C synonymous_variant 0.13
clpC1 4039530 p.Asp392Ala missense_variant 0.13
embC 4240058 p.Thr66Ala missense_variant 0.14
embC 4240076 p.Ala72Thr missense_variant 0.12
embC 4241531 p.Ile557Phe missense_variant 0.12
embC 4242077 p.Ser739Pro missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244813 p.Cys527* stop_gained 0.4
embA 4244864 c.1632G>A synonymous_variant 0.29
embA 4245187 p.Thr652Met missense_variant 0.12
embA 4245223 p.Tyr664Cys missense_variant 0.14
embA 4246042 p.Asp937Ala missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.25
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246563 p.Leu17Trp missense_variant 0.25
aftB 4267989 p.Ala283Val missense_variant 0.18
ubiA 4269130 p.Leu235Pro missense_variant 0.22
ethA 4326484 c.990T>A synonymous_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0