TB-Profiler result

Run: ERR1950086

Summary

Run ID: ERR1950086

Sample name:

Date: 31-03-2023 15:39:28

Number of reads: 556610

Percentage reads mapped: 99.33

Strain: lineage4.8

Drug-resistance: HR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
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
katG 2155142 p.Thr324Pro missense_variant 0.23 isoniazid
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 5419 c.180T>C synonymous_variant 0.15
gyrB 5607 p.Val123Gly missense_variant 0.4
gyrB 5798 p.Phe187Ile missense_variant 0.29
gyrB 6038 p.Thr267Ser missense_variant 0.3
gyrA 6362 c.-940T>C upstream_gene_variant 0.5
gyrB 6554 p.Pro439Ser missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 0.93
gyrA 8043 p.Arg248Ser missense_variant 0.4
gyrA 9014 c.1713C>A synonymous_variant 0.2
fgd1 490931 p.His50Arg missense_variant 0.14
fgd1 491468 p.Ile229Ser missense_variant 0.5
fgd1 491558 p.Lys259Thr missense_variant 0.18
mshA 575407 c.60C>T synonymous_variant 0.18
ccsA 620306 p.Val139Gly missense_variant 0.33
ccsA 620740 p.Thr284Pro missense_variant 0.17
rpoB 761289 p.Ser495Ala missense_variant 0.28
rpoC 763854 p.Val162Gly missense_variant 0.2
rpoC 764123 p.Phe252Ile missense_variant 0.5
rpoC 764943 p.His525Arg missense_variant 0.12
rpoC 765989 p.Thr874Pro missense_variant 0.23
rpoC 766651 c.3282T>G synonymous_variant 0.21
rpoC 766791 p.Val1141Gly missense_variant 0.3
rpoC 766839 p.Ile1157Ser missense_variant 0.22
rpoC 766896 p.Leu1176* stop_gained 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776952 p.Leu510Gln missense_variant 0.22
mmpL5 777269 c.1212T>G synonymous_variant 0.6
mmpR5 779452 p.Gly155Trp missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801071 p.Asp88Ala missense_variant 0.27
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303793 p.Gln288Leu missense_variant 0.18
fbiC 1304194 p.Thr422Pro missense_variant 0.2
fbiC 1304458 p.Thr510Ala missense_variant 0.25
Rv1258c 1406297 c.1044A>T synonymous_variant 0.25
Rv1258c 1406592 p.Tyr250Phe missense_variant 0.25
atpE 1461197 c.153A>G synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472395 n.550A>T non_coding_transcript_exon_variant 0.2
rrs 1472419 n.574A>T non_coding_transcript_exon_variant 0.38
rrl 1473899 n.242A>T non_coding_transcript_exon_variant 0.5
rrl 1473985 n.328A>T non_coding_transcript_exon_variant 0.29
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474050 n.393A>T non_coding_transcript_exon_variant 0.4
rrl 1474165 n.508G>T non_coding_transcript_exon_variant 0.29
rrl 1475439 n.1782A>T non_coding_transcript_exon_variant 0.25
rrl 1476648 n.2991A>T non_coding_transcript_exon_variant 0.4
inhA 1673512 c.-690C>A upstream_gene_variant 0.2
inhA 1674506 p.Gly102Ala missense_variant 0.25
inhA 1674995 p.His265Pro missense_variant 0.18
rpsA 1834121 p.Thr194Pro missense_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154097 p.Pro672Leu missense_variant 0.25
katG 2154487 p.Asp542Ala missense_variant 0.18
katG 2154955 p.Val386Gly missense_variant 0.25
katG 2155271 p.Ala281Ser missense_variant 0.18
katG 2155498 p.Leu205Arg missense_variant 0.44
katG 2155513 p.Lys200Met missense_variant 0.29
katG 2156403 c.-292A>C upstream_gene_variant 0.18
PPE35 2168140 p.Ala825Thr missense_variant 0.33
PPE35 2168143 p.Phe824Leu missense_variant 0.33
PPE35 2168372 c.2241G>T synonymous_variant 0.4
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169215 p.Glu466Asp missense_variant 0.25
PPE35 2169629 p.Asn328Lys missense_variant 0.33
PPE35 2169690 p.Gly308Val missense_variant 0.25
PPE35 2169901 p.Gly238Trp missense_variant 0.25
PPE35 2170242 p.Asn124Ser missense_variant 0.4
PPE35 2170528 p.Ser29Ala missense_variant 0.33
Rv1979c 2222093 p.Ser358Ala missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714780 p.Gln185Glu missense_variant 0.12
eis 2714923 p.Leu137* stop_gained 0.33
folC 2746262 p.Leu446Gln missense_variant 0.29
folC 2746266 p.Ser445Thr missense_variant 0.29
folC 2747081 p.Val173Ala missense_variant 0.5
ribD 2986715 c.-124T>G upstream_gene_variant 0.22
ribD 2987137 p.Val100Gly missense_variant 0.67
Rv2752c 3064670 p.Val508Leu missense_variant 0.29
Rv2752c 3064679 p.Glu505* stop_gained 0.29
Rv2752c 3064838 p.Leu452Val missense_variant 0.4
Rv2752c 3066038 p.His52Tyr missense_variant 0.25
Rv2752c 3066335 c.-144T>G upstream_gene_variant 0.2
Rv2752c 3067081 c.-890T>A upstream_gene_variant 0.2
thyX 3067555 p.Ile131Leu missense_variant 0.4
thyX 3067912 p.Ile12Leu missense_variant 0.25
thyA 3073777 p.Leu232Gln missense_variant 0.2
thyA 3074511 c.-40C>T upstream_gene_variant 0.25
thyA 3074634 c.-163G>T upstream_gene_variant 0.29
ald 3087581 c.762T>A synonymous_variant 0.25
fbiD 3339676 p.Cys187Ser missense_variant 0.4
fprA 3473873 c.-134T>C upstream_gene_variant 0.12
fbiB 3642007 p.Asn158Thr missense_variant 0.4
fbiB 3642188 c.654T>G synonymous_variant 0.2
alr 3841530 c.-110A>C upstream_gene_variant 0.2
clpC1 4038275 p.Glu810Asp missense_variant 0.15
clpC1 4039386 p.Asp440Ala missense_variant 0.21
clpC1 4040249 p.Glu152Asp missense_variant 0.22
clpC1 4040349 p.Val119Gly missense_variant 0.38
clpC1 4040379 p.Leu109* stop_gained 0.2
clpC1 4040409 p.Gly99Val missense_variant 0.15
embC 4240505 p.Ser215Thr missense_variant 0.3
embC 4240977 p.Lys372Met missense_variant 0.23
embC 4241173 p.Phe437Leu missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244005 p.Ile258Ser missense_variant 0.25
embA 4245726 p.Leu832Met missense_variant 0.2
embB 4247219 p.Leu236Val missense_variant 0.3
embB 4247690 p.Thr393Pro missense_variant 0.22
embB 4248904 c.2391G>A synonymous_variant 0.15
aftB 4267077 p.Phe587Tyr missense_variant 0.22
aftB 4267407 p.Lys477Thr missense_variant 0.17
ethA 4327143 p.Thr111Pro missense_variant 0.4
ethR 4327738 p.Tyr64Asn missense_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0