TB-Profiler result

Run: ERR270793
Summary

Run ID: ERR270793

Sample name:

Date: 31-03-2023 23:27:22

Number of reads: 1547715

Percentage reads mapped: 99.25

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 1673425 c.-15C>T upstream_gene_variant 0.94 isoniazid, ethionamide
gid 4407851 c.351delG frameshift_variant 0.94 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490669 c.-114C>T upstream_gene_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575547 p.Gly67Asp missense_variant 0.13
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777268 c.1213C>T synonymous_variant 0.17
mmpL5 777366 p.Arg372Gln missense_variant 0.14
mmpL5 777371 c.1110C>T synonymous_variant 0.14
mmpL5 777820 c.661C>T synonymous_variant 0.95
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304159 p.Val410Gly missense_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.37
rpsA 1834808 p.Arg423Cys missense_variant 0.14
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 2169320 p.Leu431Phe missense_variant 0.38
PPE35 2170214 c.399C>T synonymous_variant 0.15
PPE35 2170577 c.36G>C synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.41
folC 2747263 c.336C>A synonymous_variant 0.25
folC 2747286 p.Val105Met missense_variant 0.2
pepQ 2859791 p.Ala210Ser missense_variant 0.2
pepQ 2860063 p.Thr119Ile missense_variant 0.13
pepQ 2860147 p.Gly91Asp missense_variant 0.2
pepQ 2860211 c.207delC frameshift_variant 0.17
pepQ 2860399 p.Arg7Gln missense_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339619 p.Ala168Thr missense_variant 0.2
fbiD 3339635 p.Ser173Leu missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474928 p.Gly308Ser missense_variant 0.17
fbiB 3641921 c.387C>T synonymous_variant 0.17
fbiB 3642037 p.Ala168Val missense_variant 0.18
alr 3841473 c.-53G>A upstream_gene_variant 0.92
clpC1 4038234 p.Arg824His missense_variant 0.15
clpC1 4038857 c.1848C>A synonymous_variant 0.24
panD 4044384 c.-103C>T upstream_gene_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242415 c.-818G>A upstream_gene_variant 0.25
embC 4242422 p.Trp854Gly missense_variant 0.18
embC 4242425 p.Arg855* stop_gained 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268875 c.-39G>A upstream_gene_variant 0.13
aftB 4269735 c.-899G>A upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0