TB-Profiler result

Run: ERR2514044
Summary

Run ID: ERR2514044

Sample name:

Date: 31-03-2023 20:04:50

Number of reads: 910366

Percentage reads mapped: 99.57

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 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
katG 2155740 c.371delG frameshift_variant 0.22 isoniazid, isoniazid
ethR 4327876 p.Phe110Leu missense_variant 1.0 ethionamide
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 5484 p.Arg82Leu missense_variant 0.12
gyrA 7347 p.Glu16* stop_gained 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8345 c.1044C>T synonymous_variant 0.22
gyrA 8362 p.Arg354Leu missense_variant 0.18
gyrA 8802 p.Ala501Thr missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9746 c.2445C>T synonymous_variant 0.12
fgd1 490731 c.-52G>T upstream_gene_variant 0.14
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575325 c.-23G>T upstream_gene_variant 0.14
mshA 575999 p.Asp218Tyr missense_variant 0.13
mshA 576033 p.Gly229Asp missense_variant 0.13
mshA 576755 p.Arg470Ser missense_variant 0.4
ccsA 620133 c.243G>A synonymous_variant 0.4
ccsA 620164 c.274C>T synonymous_variant 0.14
ccsA 620503 p.Glu205* stop_gained 0.12
rpoB 759615 c.-192A>C upstream_gene_variant 0.22
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760477 p.Arg224His missense_variant 0.15
rpoB 761535 p.Pro577Thr missense_variant 0.15
rpoB 761539 p.Arg578His missense_variant 0.18
rpoB 762182 c.2380delG frameshift_variant 0.15
rpoC 763942 c.573C>T synonymous_variant 0.13
rpoC 764375 p.Ala336Ser missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776777 c.1704C>A synonymous_variant 0.15
mmpL5 777269 c.1212T>C synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781505 c.-55G>T upstream_gene_variant 0.14
rplC 800889 c.81C>A synonymous_variant 1.0
rplC 801166 p.Gly120Ser missense_variant 0.15
fbiC 1303100 p.Asp57Ala missense_variant 0.12
fbiC 1303251 p.Phe107Leu missense_variant 0.13
fbiC 1304797 p.Ala623Thr missense_variant 0.12
fbiC 1304838 p.Met636Ile missense_variant 0.4
Rv1258c 1406520 p.Gly274Val missense_variant 0.14
Rv1258c 1407000 p.Ala114Gly missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473773 n.116C>T non_coding_transcript_exon_variant 0.17
rrl 1474104 n.447G>T non_coding_transcript_exon_variant 0.12
rrl 1474514 n.857G>T non_coding_transcript_exon_variant 0.12
rrl 1474799 n.1142G>A non_coding_transcript_exon_variant 0.13
rrl 1475423 n.1766T>C non_coding_transcript_exon_variant 0.1
fabG1 1673898 p.Tyr153* stop_gained 0.19
inhA 1674394 p.Val65Met missense_variant 0.11
tlyA 1917877 c.-63T>C upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101711 c.1332G>A synonymous_variant 0.18
ndh 2102256 p.Asp263Tyr missense_variant 0.18
ndh 2103035 p.Pro3Leu missense_variant 1.0
katG 2154025 p.Leu696Pro missense_variant 0.11
katG 2155986 c.126G>A synonymous_variant 0.14
PPE35 2168303 c.2310G>T synonymous_variant 1.0
PPE35 2170372 p.Thr81Ala missense_variant 0.1
Rv1979c 2222619 c.546G>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289630 c.-389G>T upstream_gene_variant 0.25
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518765 c.651G>T synonymous_variant 0.12
kasA 2519324 p.Phe404Leu missense_variant 0.11
eis 2715426 c.-94G>T upstream_gene_variant 0.12
ahpC 2726738 p.Asp182Glu missense_variant 0.13
folC 2746613 p.Gly329Val missense_variant 0.33
folC 2746635 p.Asp322Tyr missense_variant 0.4
folC 2747794 c.-196A>T upstream_gene_variant 0.15
pepQ 2859901 p.Ser173Asn missense_variant 0.15
pepQ 2860006 p.Gly138Asp missense_variant 0.12
pepQ 2860104 c.315C>T synonymous_variant 0.2
ribD 2987246 c.408C>A synonymous_variant 0.5
Rv2752c 3065689 p.Thr168Ile missense_variant 0.13
Rv2752c 3067109 c.-918T>C upstream_gene_variant 0.11
Rv2752c 3067157 c.-966G>T upstream_gene_variant 0.13
thyX 3067442 c.503delG frameshift_variant 0.12
thyA 3074547 c.-76G>A upstream_gene_variant 0.17
thyA 3074590 c.-119C>T upstream_gene_variant 0.15
thyA 3074593 c.-122C>T upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339459 c.342A>G synonymous_variant 0.18
fbiD 3339654 c.537A>G synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474968 p.Ser321Leu missense_variant 0.22
whiB7 3568834 c.-155G>T upstream_gene_variant 0.11
Rv3236c 3612351 p.Ala256Thr missense_variant 0.14
Rv3236c 3612412 c.705G>T synonymous_variant 0.15
Rv3236c 3612582 p.Leu179Val missense_variant 0.12
Rv3236c 3612752 p.Ala122Gly missense_variant 0.12
Rv3236c 3612760 c.357C>T synonymous_variant 0.12
fbiB 3641175 c.-360G>A upstream_gene_variant 0.2
fbiA 3641491 p.Ala317Thr missense_variant 0.12
fbiB 3641709 p.Arg59Trp missense_variant 0.12
fbiB 3641938 p.Gly135Glu missense_variant 0.18
fbiB 3641985 p.Thr151Ala missense_variant 0.14
fbiB 3642816 p.Tyr428His missense_variant 0.14
alr 3840263 c.1158C>T synonymous_variant 1.0
alr 3840526 p.Trp299Arg missense_variant 0.13
alr 3840937 p.Leu162Met missense_variant 0.14
rpoA 3878364 c.144A>G synonymous_variant 0.11
rpoA 3878644 c.-137G>A upstream_gene_variant 0.5
ddn 3986875 p.Ser11Leu missense_variant 0.12
clpC1 4038878 c.1827A>G synonymous_variant 0.11
clpC1 4039530 p.Asp392Ala missense_variant 0.1
clpC1 4039594 p.Arg371Gly missense_variant 0.12
clpC1 4039829 p.Leu292Phe missense_variant 0.12
embC 4239674 c.-189C>A upstream_gene_variant 0.12
embC 4240441 p.Phe193Leu missense_variant 0.2
embC 4240475 p.Ala205Ser missense_variant 1.0
embC 4240954 c.1096delC frameshift_variant 0.13
embC 4242365 c.2506delC frameshift_variant 0.17
embC 4242587 p.Gly909Arg missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243610 c.378G>A synonymous_variant 0.29
embA 4243888 p.Val219Gly missense_variant 0.22
embA 4243932 p.Arg234Cys missense_variant 0.4
embA 4243954 p.Arg241Leu missense_variant 0.25
embA 4243967 c.735G>T synonymous_variant 0.22
embA 4244009 c.777G>T synonymous_variant 0.29
embA 4244049 p.Asp273Asn missense_variant 0.25
embA 4244189 c.957C>T synonymous_variant 0.15
embA 4245741 c.2513delC frameshift_variant 0.12
embB 4246124 c.-390G>A upstream_gene_variant 0.5
embA 4246488 p.Arg1086Trp missense_variant 0.14
embB 4246925 p.Glu138* stop_gained 0.2
embB 4247426 p.Gly305Thr missense_variant 0.13
embB 4247887 c.1374C>T synonymous_variant 0.17
embB 4247899 p.Met462Ile missense_variant 0.13
embB 4248465 p.Ser651Asn missense_variant 0.11
embB 4249638 p.Leu1042Pro missense_variant 0.13
embB 4249695 p.Trp1061Ser missense_variant 0.11
aftB 4267091 c.1746C>A synonymous_variant 1.0
aftB 4267549 p.Leu430Phe missense_variant 0.4
aftB 4267812 p.Pro342Leu missense_variant 0.17
aftB 4268127 p.Pro237Leu missense_variant 0.14
aftB 4268605 p.Arg78Cys missense_variant 0.22
aftB 4268777 c.60G>C synonymous_variant 0.11
ubiA 4268991 p.Asp281Glu missense_variant 0.11
ubiA 4269215 p.Arg207Cys missense_variant 0.14
ethR 4327631 p.Ala28Val missense_variant 0.17
whiB6 4338270 c.252A>G synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0