TB-Profiler result

Run: ERR4815716
Summary

Run ID: ERR4815716

Sample name:

Date: 01-04-2023 14:01:25

Number of reads: 282966

Percentage reads mapped: 60.32

Strain:

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
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 2155433 c.678delG frameshift_variant 0.29 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 6124 c.885C>T synonymous_variant 1.0
gyrB 7124 p.Ser629Ala missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7871 c.572dupC frameshift_variant 0.4
gyrA 8437 p.Tyr379Cys missense_variant 0.18
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9047 c.1746C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576000 p.Asp218Ala missense_variant 1.0
mshA 576579 p.Gly411Glu missense_variant 0.33
ccsA 619916 p.Gly9Asp missense_variant 0.22
rpoB 760471 p.Arg222His missense_variant 0.5
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 760929 p.Val375Phe missense_variant 0.5
rpoB 761279 c.1473C>A synonymous_variant 0.29
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 764355 p.Gln329Pro missense_variant 0.4
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779267 c.280dupC frameshift_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406890 p.Asn151Asp missense_variant 0.15
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833414 c.-127delT upstream_gene_variant 0.4
rpsA 1833692 p.Val51Leu missense_variant 0.67
rpsA 1834499 p.Leu320Met missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101672 c.1371A>G synonymous_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167654 p.Pro987Ser missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167930 p.Ser895Pro missense_variant 0.5
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169592 p.Ile341Val missense_variant 0.18
PPE35 2169691 p.Gly308Ser missense_variant 1.0
PPE35 2170325 c.287delA frameshift_variant 0.23
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746633 c.965delA frameshift_variant 0.4
folC 2747003 p.Ile199Thr missense_variant 0.2
ribD 2986640 c.-199C>T upstream_gene_variant 0.29
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065305 p.Ala296Val missense_variant 1.0
Rv2752c 3065444 p.Asp250His missense_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339378 p.Asp87Glu missense_variant 0.29
Rv3083 3448319 c.-185C>T upstream_gene_variant 0.33
Rv3083 3449018 p.Asp172Gly missense_variant 0.4
Rv3083 3449323 p.Arg274* stop_gained 0.67
Rv3083 3449353 p.Ser284Gly missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474102 c.96C>A synonymous_variant 0.18
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3640965 c.-570C>A upstream_gene_variant 0.17
fbiB 3642206 c.672C>T synonymous_variant 0.2
rpoA 3878082 c.426T>C synonymous_variant 0.4
rpoA 3878705 c.-198A>G upstream_gene_variant 1.0
clpC1 4039071 p.Pro545Gln missense_variant 0.5
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240126 p.Cys88* stop_gained 0.25
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242304 c.-929G>A upstream_gene_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 c.2964delG frameshift_variant 0.25
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244234 c.1003dupT frameshift_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269692 p.Tyr48His missense_variant 0.25
ethR 4326577 c.-972G>T upstream_gene_variant 1.0
ethA 4328243 c.-770C>T upstream_gene_variant 0.25
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407964 p.Ala80Glu missense_variant 0.2
gid 4407990 c.213A>G synonymous_variant 0.2