TB-Profiler result

Run: SRR11972452
Summary

Run ID: SRR11972452

Sample name:

Date: 03-04-2023 05:43:31

Number of reads: 952945

Percentage reads mapped: 98.56

Strain: lineage1.1.3.1

Drug-resistance: MDR-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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.1 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
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4248003 p.Gln497Arg missense_variant 1.0 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 5117 c.-123G>A upstream_gene_variant 0.67
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6436 c.-866C>T upstream_gene_variant 1.0
gyrB 7161 p.Ala641Asp 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 8560 p.Gly420Val missense_variant 0.12
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9639 p.Gly780Ser missense_variant 0.14
fgd1 491105 p.Gly108Asp missense_variant 0.12
fgd1 491320 p.Ala180Ser missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
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 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777106 p.Ser459Pro missense_variant 0.11
mmpL5 777572 c.909C>T synonymous_variant 0.91
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 1673346 c.-94C>G upstream_gene_variant 0.18
fabG1 1673349 c.-91G>C upstream_gene_variant 0.18
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.34
inhA 1674371 p.Lys57Thr missense_variant 0.12
inhA 1674828 p.Glu209Asp missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102468 p.Leu192Pro missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155656 p.Lys152Asn missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.35
PPE35 2170053 p.Thr187Ser missense_variant 0.41
PPE35 2170349 p.Thr88Ala missense_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290082 c.-841A>T upstream_gene_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064640 c.1552T>C synonymous_variant 0.18
thyX 3067467 p.Ala160Val missense_variant 0.14
thyX 3067539 p.Ala136Val missense_variant 0.12
ald 3086750 c.-70A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449134 p.Gln211Lys missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474388 p.Phe128Leu missense_variant 0.17
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474706 p.Thr234Ala missense_variant 0.18
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3641404 p.Trp288Arg missense_variant 0.29
fbiB 3641407 c.-128C>T upstream_gene_variant 0.29
alr 3840689 c.732C>T synonymous_variant 1.0
alr 3841253 c.168C>T synonymous_variant 1.0
alr 3841277 c.144C>T synonymous_variant 1.0
clpC1 4039485 p.Gly407Asp missense_variant 0.11
clpC1 4039730 c.975C>G synonymous_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044278 c.4T>C synonymous_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241256 p.Arg465Met missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248762 p.Ala750Asp missense_variant 0.17
embB 4249677 p.Arg1055His missense_variant 0.17
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4327450 c.-99G>A upstream_gene_variant 1.0
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 4408103 p.Gly34Arg missense_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0