TB-Profiler result

Run: SRR12199423
Summary

Run ID: SRR12199423

Sample name:

Date: 03-04-2023 06:38:54

Number of reads: 801939

Percentage reads mapped: 98.83

Strain: lineage1.2.2.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 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
kasA 2519274 p.Gly387Asp 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
gyrB 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6960 p.Gln574Arg missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575830 c.483C>T synonymous_variant 0.12
mshA 576305 p.Gly320Ser missense_variant 0.12
mshA 576452 p.Val369Leu missense_variant 0.17
ccsA 620271 c.381C>A synonymous_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 765570 p.Ala734Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.19
PPE35 2169910 p.Asn235Tyr missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.37
PPE35 2170053 p.Thr187Ser missense_variant 0.37
PPE35 2170372 p.Thr81Ala missense_variant 0.1
PPE35 2170512 p.Leu34Arg missense_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290155 c.-914G>T upstream_gene_variant 0.11
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519311 c.1197C>T synonymous_variant 0.16
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746443 p.Asp386Tyr missense_variant 0.12
folC 2746631 p.Gly323Asp missense_variant 0.14
thyX 3067611 p.Lys112Arg missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474993 c.987G>A synonymous_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612880 c.237G>T synonymous_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.16
clpC1 4039419 p.Ala429Asp missense_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242485 p.Glu875Gln missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268036 p.Trp267Cys missense_variant 0.12
aftB 4268228 c.609C>T synonymous_variant 0.22
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys missense_variant 0.94
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0