TB-Profiler result

Run: ERR2229494
Summary

Run ID: ERR2229494

Sample name:

Date: 31-03-2023 17:15:16

Number of reads: 519526

Percentage reads mapped: 99.04

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 2156108 p.Pro2Ser missense_variant 0.12 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 490712 c.-71T>C upstream_gene_variant 0.14
mshA 576579 p.Gly411Val missense_variant 0.25
ccsA 620069 p.Thr60Asn missense_variant 0.17
rpoB 762334 p.Gly843Asp missense_variant 0.17
rpoB 763231 p.Arg1142His missense_variant 0.12
rpoC 767113 c.3744G>A synonymous_variant 0.25
rpoC 767118 p.Glu1250Val missense_variant 0.25
rpoC 767192 p.Thr1275Ala missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775744 p.Gly913Ser missense_variant 0.17
mmpL5 776009 c.2472A>G synonymous_variant 0.25
mmpL5 776018 c.2463G>C synonymous_variant 0.33
mmpL5 776021 c.2460G>C synonymous_variant 0.2
mmpL5 776348 c.2133G>A synonymous_variant 0.22
mmpL5 777164 c.1317C>T synonymous_variant 0.25
mmpL5 777173 c.1308C>T synonymous_variant 0.29
mmpL5 777176 p.Glu435Asp missense_variant 0.29
mmpS5 778803 p.Glu35* stop_gained 0.22
mmpR5 779334 p.Gln115His missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801100 p.Gly98Arg missense_variant 0.4
fbiC 1302802 c.-129G>C upstream_gene_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471848 n.3T>C non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475466 n.1809A>T non_coding_transcript_exon_variant 0.25
rrl 1475590 n.1933A>T non_coding_transcript_exon_variant 0.18
fabG1 1673213 c.-227A>T upstream_gene_variant 0.14
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.17
fabG1 1673361 c.-79C>G upstream_gene_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.42
fabG1 1673848 p.Phe137Ile missense_variant 0.2
inhA 1674980 p.Ala260Val missense_variant 0.2
rpsA 1834333 c.792C>T synonymous_variant 0.4
tlyA 1917934 c.-6T>C upstream_gene_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101985 p.Gly353Val missense_variant 0.22
katG 2154513 c.1599G>T synonymous_variant 0.15
katG 2155099 p.Gly338Val missense_variant 0.17
PPE35 2168047 p.Leu856Val missense_variant 0.25
PPE35 2168051 p.Val854Ile missense_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.29
PPE35 2169272 c.1341C>G synonymous_variant 0.29
PPE35 2169278 c.1335T>C synonymous_variant 0.32
PPE35 2169281 c.1332T>G synonymous_variant 0.33
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.52
PPE35 2170528 p.Ser29Ala missense_variant 0.15
Rv1979c 2222287 p.Ala293Glu missense_variant 0.2
Rv1979c 2222647 p.Ala173Glu missense_variant 0.17
Rv1979c 2222881 p.Gly95Val missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290026 c.-785C>A upstream_gene_variant 0.22
kasA 2518798 c.684G>C synonymous_variant 0.18
kasA 2518801 c.687G>A synonymous_variant 0.18
kasA 2518809 p.Lys232Arg missense_variant 0.17
kasA 2519140 c.1026G>C synonymous_variant 0.29
kasA 2519143 c.1029G>C synonymous_variant 0.29
ahpC 2725956 c.-237G>T upstream_gene_variant 0.33
folC 2746414 p.Glu395Asp missense_variant 0.4
folC 2746657 c.942T>C synonymous_variant 0.67
pepQ 2859923 p.Gly166Cys missense_variant 0.17
Rv2752c 3064799 p.Arg465Trp missense_variant 0.2
thyX 3067943 c.3G>T synonymous_variant 0.33
thyA 3074637 c.-166A>G upstream_gene_variant 0.5
fbiD 3339364 p.Pro83Ala missense_variant 0.2
fbiB 3642321 p.Val263Phe missense_variant 0.2
alr 3840239 c.1181delC frameshift_variant 0.29
alr 3841539 c.-119C>T upstream_gene_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.18
rpoA 3877862 p.Val216Phe missense_variant 0.33
ddn 3986975 c.132T>C synonymous_variant 0.11
clpC1 4038289 p.Asn806Tyr missense_variant 0.17
clpC1 4038420 p.Arg762His missense_variant 0.22
clpC1 4038511 p.Asp732Asn missense_variant 0.2
panD 4043892 c.390G>A synonymous_variant 0.13
panD 4044301 c.-20G>T upstream_gene_variant 0.29
embC 4241727 p.Phe622Tyr missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.75
embB 4246555 c.42G>C synonymous_variant 0.75
embB 4246556 p.Ala15Pro missense_variant 0.75
embB 4246563 p.Leu17Trp missense_variant 0.67
embB 4246567 c.54G>T synonymous_variant 0.5
embB 4247068 c.555T>C synonymous_variant 0.4
embB 4249297 c.2784G>A synonymous_variant 0.15
embB 4249506 p.Gln998Pro missense_variant 0.18
embB 4249598 p.Glu1029Lys missense_variant 0.2
aftB 4267990 p.Ala283Thr missense_variant 0.33
ubiA 4269161 p.Ser225Thr missense_variant 0.2
ethA 4326686 p.Met263Thr missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407911 p.Thr98Ser missense_variant 0.2