TB-Profiler result

Run: ERR8158019
Summary

Run ID: ERR8158019

Sample name:

Date: 02-04-2023 07:20:52

Number of reads: 432440

Percentage reads mapped: 99.61

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 2155788 p.His108Gln missense_variant 0.14 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 7220 p.Ser661Gly missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7374 p.Gln25Lys missense_variant 0.14
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8972 p.His557Gln missense_variant 0.12
gyrA 9259 p.Leu653Gln missense_variant 0.12
gyrA 9275 p.Glu658Asp missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9323 c.2022C>T synonymous_variant 0.12
fgd1 491444 p.Ser221Phe missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575580 c.235delC frameshift_variant 0.18
ccsA 620176 p.Val96Leu missense_variant 0.33
ccsA 620528 p.Ala213Glu missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759805 c.-2T>A upstream_gene_variant 0.11
rpoB 762210 p.Pro802Thr missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765106 c.1737G>A synonymous_variant 0.15
rpoC 767230 c.3861G>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775952 c.2529G>T synonymous_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777472 p.Val337Met missense_variant 1.0
mmpL5 777587 c.894G>C synonymous_variant 0.13
mmpL5 778070 p.Thr137Ala missense_variant 0.14
mmpR5 778079 c.-911C>G upstream_gene_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781372 c.-188T>C upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801330 c.522G>T synonymous_variant 0.11
fbiC 1302786 c.-144delT upstream_gene_variant 0.15
fbiC 1302793 c.-138A>G upstream_gene_variant 0.18
fbiC 1304148 c.1218C>A synonymous_variant 0.22
fbiC 1304390 p.Ala487Asp missense_variant 0.11
Rv1258c 1406261 c.1080C>A synonymous_variant 0.2
Rv1258c 1406598 p.Pro248Gln missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406769 c.571delC frameshift_variant 0.17
Rv1258c 1407055 c.285dupG frameshift_variant 0.22
Rv1258c 1407326 p.Asn5Lys missense_variant 0.24
Rv1258c 1407352 c.-12G>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472528 n.683T>G non_coding_transcript_exon_variant 0.11
rrs 1472950 n.1105C>A non_coding_transcript_exon_variant 0.14
rrl 1474133 n.476T>C non_coding_transcript_exon_variant 0.14
rrl 1474964 n.1309delG non_coding_transcript_exon_variant 0.15
rrl 1476470 n.2813C>A non_coding_transcript_exon_variant 0.22
fabG1 1673483 p.Ser15Tyr missense_variant 0.13
inhA 1674415 p.Ala72Pro missense_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834615 c.1074C>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155565 p.Phe183Leu missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169562 c.1047_1050delTGGC frameshift_variant 1.0
PPE35 2169775 p.Ala280Thr missense_variant 0.14
PPE35 2170232 c.381T>A synonymous_variant 0.2
PPE35 2170561 p.Gly18Trp missense_variant 0.14
Rv1979c 2222507 p.Ser220Cys missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518002 c.-113C>A upstream_gene_variant 0.11
kasA 2518008 c.-107C>G upstream_gene_variant 0.11
kasA 2518070 c.-45C>T upstream_gene_variant 0.18
kasA 2518470 p.Ala119Val missense_variant 0.12
kasA 2518807 c.693C>T synonymous_variant 0.11
eis 2714807 p.Glu176* stop_gained 0.11
eis 2715574 c.-242T>C upstream_gene_variant 0.13
folC 2747319 p.Gly94Ser missense_variant 0.2
Rv2752c 3064759 p.Val478Ala missense_variant 0.12
Rv2752c 3065585 p.Ser203Pro missense_variant 0.14
thyA 3074370 p.Met34Ile missense_variant 0.12
thyA 3074479 c.-8T>C upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086855 p.Asn12Lys missense_variant 0.12
ald 3086991 p.Val58Phe missense_variant 0.2
Rv3083 3448321 c.-183G>A upstream_gene_variant 0.33
Rv3083 3448638 p.Trp45Cys missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612195 p.Thr308Ala missense_variant 0.11
Rv3236c 3612323 p.Pro265Leu missense_variant 0.12
Rv3236c 3612771 p.Val116Phe missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613098 p.Leu7Met missense_variant 0.13
Rv3236c 3613170 c.-54G>T upstream_gene_variant 0.15
Rv3236c 3613267 c.-151G>A upstream_gene_variant 0.15
fbiA 3640777 c.238_239delGG frameshift_variant 0.11
fbiB 3642267 p.Thr245Ser missense_variant 0.15
rpoA 3878037 c.471C>A synonymous_variant 0.12
ddn 3987002 c.159C>A synonymous_variant 0.18
ddn 3987019 p.Pro59Gln missense_variant 0.18
ddn 3987167 c.324C>T synonymous_variant 0.14
clpC1 4038595 p.His704Tyr missense_variant 0.11
clpC1 4039283 p.Asp474Glu missense_variant 0.13
clpC1 4039334 c.1371G>T synonymous_variant 0.11
clpC1 4039616 c.1089G>A synonymous_variant 0.13
clpC1 4040407 p.His100Asn missense_variant 0.13
panD 4044015 c.267G>A synonymous_variant 0.13
embC 4240542 p.Thr227Lys missense_variant 0.29
embC 4241029 p.Trp389Cys missense_variant 0.15
embC 4241419 p.Tyr519* stop_gained 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243130 p.Pro1090Thr missense_variant 0.12
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243625 c.393C>T synonymous_variant 0.18
embA 4243657 p.Trp142Leu missense_variant 0.14
embA 4243902 p.Leu224Met missense_variant 0.12
embA 4244433 p.Ala401Ser missense_variant 0.29
embA 4244859 p.Gly543Trp missense_variant 0.15
embA 4244967 p.Gly579Arg missense_variant 0.25
embB 4247384 p.His291Asn missense_variant 0.11
embB 4248432 p.Trp640Leu missense_variant 0.11
embB 4248788 p.Thr759Ser missense_variant 0.15
embB 4248805 p.Met764Ile missense_variant 0.12
embB 4249195 c.2682C>A synonymous_variant 0.12
embB 4249717 c.3204C>T synonymous_variant 0.4
aftB 4267300 p.Pro513Ser missense_variant 0.14
aftB 4267305 c.1531delG frameshift_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268487 p.Met117Arg missense_variant 0.14
ubiA 4269111 p.Asp241Glu missense_variant 0.1
ethA 4326517 c.957G>T synonymous_variant 0.11
ethA 4326676 p.Ser266Arg missense_variant 1.0
ethA 4326858 p.Gln206Lys missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407810 p.Ser131Arg missense_variant 0.11
gid 4407927 p.Glu92Asp missense_variant 1.0