TB-Profiler result

Run: ERR11068581
Summary

Run ID: ERR11068581

Sample name:

Date: 06-04-2023 18:12:13

Number of reads: 3828719

Percentage reads mapped: 98.94

Strain: lineage1.1.2

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
lineage1.1.2 Indo-Oceanic EAI3;EAI5 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155783 p.Ala110Val missense_variant 0.22 isoniazid
pncA 2288826 p.Val139Ala missense_variant 1.0 pyrazinamide
ethA 4326589 c.884delT frameshift_variant 1.0 ethionamide, ethionamide
thyA 3071476 c.-444_*2203del transcript_ablation 1.0 para-aminosalicylic_acid
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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_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 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 575223 c.-125G>A upstream_gene_variant 0.13
mshA 576000 p.Asp218Ala missense_variant 1.0
mshA 576116 p.Ala257Pro missense_variant 0.4
mshA 576119 p.Ala258Pro missense_variant 0.44
mshA 576217 c.870G>A synonymous_variant 0.22
mshA 576259 c.912C>T synonymous_variant 0.33
mshA 576456 p.Val370Gly missense_variant 1.0
ccsA 619916 p.Gly9Asp missense_variant 0.15
rpoB 760490 c.684C>T 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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406212 p.His377Tyr missense_variant 0.17
Rv1258c 1406837 c.504T>A synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674803 p.Ala201Val missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918540 p.Pro201Ser missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
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 2519167 c.1053T>C synonymous_variant 0.12
eis 2714839 p.Leu165Trp missense_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746863 c.736C>T synonymous_variant 0.13
folC 2747386 c.213C>T synonymous_variant 0.14
pepQ 2859813 p.Ile202Met missense_variant 0.12
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065305 p.Ala296Val missense_variant 1.0
thyX 3067965 c.-20C>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087335 c.516G>A synonymous_variant 0.17
fbiD 3339074 c.-44C>T upstream_gene_variant 0.11
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 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3642077 p.Asp181Glu missense_variant 0.12
rpoA 3878590 c.-83G>C upstream_gene_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240425 p.Arg188His missense_variant 0.12
embC 4240444 c.582C>T synonymous_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243532 c.300C>T synonymous_variant 0.33
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244902 p.Ala557Val missense_variant 0.15
embA 4245661 p.Ala810Val missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246041 p.Asp937Asn missense_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247649 p.Ala379Val missense_variant 0.17
embB 4247846 p.Gln445* stop_gained 0.17
embB 4248254 p.Thr581Ala missense_variant 1.0
aftB 4267939 p.Arg300Trp missense_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_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