TB-Profiler result

Run: ERR11049930
Summary

Run ID: ERR11049930

Sample name:

Date: 02-04-2023 03:32:25

Number of reads: 3544988

Percentage reads mapped: 99.3

Strain: lineage1.2.2.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.1 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 0.99 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
gid 4408115 c.87delC frameshift_variant 1.0 streptomycin
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
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 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576113 p.Arg256Gly missense_variant 0.23
mshA 576442 p.Cys365Trp missense_variant 0.21
mshA 576453 p.Val369Gly missense_variant 0.22
mshA 576613 c.1266A>C synonymous_variant 0.33
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.24
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
fabG1 1673553 p.Asp38Glu missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103055 c.-13G>A upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.23
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.22
kasA 2519353 p.Phe413Leu missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.13
Rv2752c 3064823 p.Val457Leu missense_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.67
fbiD 3339749 p.Val211Gly missense_variant 0.29
fbiD 3339751 p.Ala212Pro missense_variant 0.25
Rv3083 3448714 p.Asp71His missense_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.33
rpoA 3878641 c.-134C>G upstream_gene_variant 0.85
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.32
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.37
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248328 c.1815G>C synonymous_variant 0.29
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 0.99
whiB6 4338200 p.Asp108His missense_variant 0.16
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