TB-Profiler result

Run: SRR6045206
Summary

Run ID: SRR6045206

Sample name:

Date: 04-04-2023 11:54:43

Number of reads: 599379

Percentage reads mapped: 48.73

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 0.99
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
fabG1 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
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 1.0
fgd1 491554 p.Gln258* stop_gained 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760434 p.Val210Ile missense_variant 0.13
rpoB 761837 p.Cys677* stop_gained 0.12
rpoC 762737 c.-633C>T upstream_gene_variant 0.12
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 764080 c.711C>T synonymous_variant 0.13
rpoC 766954 c.3585C>T synonymous_variant 0.14
rpoC 766969 c.3600C>T synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777623 p.Gln286His missense_variant 0.12
mmpL5 778612 c.-132C>T upstream_gene_variant 0.12
rpsL 781385 c.-175C>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407527 c.-187G>A upstream_gene_variant 0.15
embR 1416713 p.Ile212Thr missense_variant 0.1
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473401 n.-257G>A upstream_gene_variant 0.25
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 2168031 p.Thr861Lys missense_variant 0.11
PPE35 2168205 p.Pro803Gln missense_variant 1.0
PPE35 2168775 p.Pro613Leu missense_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289358 c.-117T>G upstream_gene_variant 0.17
pncA 2289468 c.-227G>T upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519217 p.Pro368Leu missense_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2859886 p.Ala178Asp missense_variant 0.15
Rv2752c 3065165 p.Gly343Ser missense_variant 0.12
Rv2752c 3066301 c.-111dupC upstream_gene_variant 0.1
Rv2752c 3067032 c.-841C>A upstream_gene_variant 0.12
thyX 3067238 c.708C>T synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086929 p.Ala37Val missense_variant 0.15
Rv3083 3448700 p.Phe66Ser missense_variant 0.12
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 3474653 p.Ala216Val missense_variant 0.13
fprA 3474911 p.Val302Ala missense_variant 0.17
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612804 p.Ala105Thr missense_variant 1.0
fbiA 3640579 p.Ala13Thr missense_variant 0.12
fbiB 3642785 c.1251C>T synonymous_variant 0.15
fbiB 3642800 c.1266C>T synonymous_variant 0.13
rpoA 3878483 c.25C>T synonymous_variant 0.12
rpoA 3878561 c.-54C>T upstream_gene_variant 0.5
ddn 3987184 p.Ala114Val missense_variant 0.11
clpC1 4039062 p.Ser548Leu missense_variant 0.17
clpC1 4039654 p.Thr351Ser missense_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044307 c.-26A>G upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4241022 p.Ala387Val missense_variant 0.12
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242653 p.Ala931Thr missense_variant 0.14
embC 4242671 p.Pro937Ser missense_variant 0.15
embA 4243474 p.Thr81Met missense_variant 0.12
embA 4243532 c.300C>A synonymous_variant 1.0
embA 4243539 p.Ala103Thr missense_variant 0.13
embA 4243721 c.489G>A synonymous_variant 0.13
embA 4244282 c.1050C>A synonymous_variant 0.15
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246275 p.Ala1015Thr missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248343 c.1830G>T synonymous_variant 0.13
embB 4249330 p.Met939Ile missense_variant 0.27
aftB 4267835 p.Met334Ile missense_variant 0.15
aftB 4268614 p.Gly75Arg missense_variant 0.18
aftB 4268630 p.Val69Ile missense_variant 0.14
aftB 4268811 p.Ser9Leu missense_variant 0.11
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269469 p.Pro122Gln missense_variant 0.94
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
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
gid 4408124 p.Ala27Pro missense_variant 1.0