TB-Profiler result

Run: ERR4820912
Summary

Run ID: ERR4820912

Sample name:

Date: 01-04-2023 16:57:11

Number of reads: 482405

Percentage reads mapped: 99.39

Strain: lineage1.1.3.1

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3.1 Indo-Oceanic NA RD239 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 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
thyA 3074095 p.Arg126Gln missense_variant 0.5 para-aminosalicylic_acid
embB 4247618 p.Val369Leu missense_variant 0.17 ethambutol
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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9261 p.Arg654Cys missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575601 p.Glu85Gly missense_variant 0.22
ccsA 620070 c.180C>T synonymous_variant 0.2
rpoB 760373 c.567C>T synonymous_variant 0.13
rpoB 760747 p.Leu314Pro missense_variant 0.25
rpoB 761083 p.Gly426Val missense_variant 0.33
rpoB 762540 p.Asn912Tyr missense_variant 0.18
rpoB 762559 p.Arg918Gln missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765089 c.1720T>C synonymous_variant 0.13
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 766003 c.2634G>T synonymous_variant 0.11
rpoC 766269 p.Thr967Met missense_variant 0.12
rpoC 767280 p.Ala1304Val missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776213 c.2268C>A synonymous_variant 0.14
mmpL5 777406 p.Ala359Thr missense_variant 0.22
mmpS5 779502 c.-597T>A upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302960 c.30C>T synonymous_variant 0.14
fbiC 1303275 c.345C>A synonymous_variant 0.2
fbiC 1304198 p.Gly423Asp missense_variant 0.12
fbiC 1304386 p.Arg486Gly missense_variant 0.22
fbiC 1305248 p.Ala773Val missense_variant 0.11
Rv1258c 1407106 p.Asp79Tyr missense_variant 0.15
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471661 n.-185C>T upstream_gene_variant 0.67
inhA 1674630 c.429C>A synonymous_variant 0.18
rpsA 1834494 p.Glu318Gly missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918092 c.153G>A synonymous_variant 0.25
ndh 2102820 p.Val75Met missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154770 p.Asp448Asn missense_variant 0.15
PPE35 2167789 p.Gly942Ser missense_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222804 p.Ala121Thr missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289457 c.-217dupG upstream_gene_variant 0.22
pncA 2290051 c.-810C>T upstream_gene_variant 0.25
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747133 p.Thr156Ser missense_variant 0.18
folC 2747482 c.117G>A synonymous_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065033 p.Gly387Arg missense_variant 0.11
thyX 3067513 p.Glu145Lys missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448403 c.-100delC upstream_gene_variant 0.2
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449812 p.Asp437Asn missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474217 p.Ala71Thr missense_variant 0.4
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474961 p.Val319Met missense_variant 0.22
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612159 p.Arg320Trp missense_variant 0.13
fbiB 3640695 c.-840C>T upstream_gene_variant 1.0
fbiA 3641311 p.Asp257Asn missense_variant 0.13
fbiB 3641993 c.459A>G synonymous_variant 0.14
fbiB 3642052 p.Leu173Gln missense_variant 0.12
alr 3840688 p.Asp245Asn missense_variant 1.0
alr 3841162 p.Ala87Thr missense_variant 0.13
alr 3841253 c.168C>T synonymous_variant 1.0
clpC1 4038324 p.Val794Ala missense_variant 0.17
clpC1 4038469 p.Asp746Tyr missense_variant 0.2
clpC1 4039048 p.Gly553Ser missense_variant 0.29
clpC1 4039938 p.Val256Glu missense_variant 0.18
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040752 c.-48C>T upstream_gene_variant 0.29
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244288 c.1056C>T synonymous_variant 0.5
embA 4244712 p.Ala494Ser missense_variant 0.17
embA 4245102 p.Trp624Gly missense_variant 0.14
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246029 p.Pro933Thr missense_variant 0.25
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267990 p.Ala283Ser missense_variant 0.22
aftB 4268012 c.825G>T synonymous_variant 0.17
aftB 4268015 c.822G>T synonymous_variant 0.17
aftB 4268316 p.Ala174Val missense_variant 1.0
aftB 4268448 p.Pro130Leu missense_variant 0.11
ubiA 4269014 p.Pro274Ser missense_variant 0.22
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327416 p.Ala20Thr missense_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408039 p.Ile55Asn missense_variant 1.0
gid 4408055 c.148C>T synonymous_variant 1.0