TB-Profiler result

Run: ERR245777
Summary

Run ID: ERR245777

Sample name:

Date: 31-03-2023 18:20:49

Number of reads: 14479150

Percentage reads mapped: 99.48

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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
fabG1 1673425 c.-15C>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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.24
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.34
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767305 p.Tyr1312* stop_gained 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.23
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.22
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.2
inhA 1674892 p.Asn231Asp missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.27
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156159 c.-48C>G upstream_gene_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.3
PPE35 2170461 p.Gly51Glu missense_variant 0.99
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
eis 2714366 p.Val323Leu missense_variant 0.24
eis 2715586 c.-254G>C upstream_gene_variant 0.45
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.22
pepQ 2859974 p.Ala149Pro missense_variant 0.24
Rv2752c 3064552 p.Arg547Pro missense_variant 0.21
Rv2752c 3064741 p.Gly484Ala missense_variant 0.28
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339550 p.Gly145Trp missense_variant 0.26
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.24
fbiB 3642734 c.1200G>C synonymous_variant 0.22
clpC1 4038857 c.1848C>A synonymous_variant 0.21
clpC1 4039932 p.Gly258Val missense_variant 0.34
embC 4239842 c.-21C>A upstream_gene_variant 0.15
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.14
embC 4242476 p.Pro872Ala missense_variant 0.31
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.36
embC 4242827 p.Leu989Val missense_variant 0.17
ubiA 4269529 p.Ala102Gly missense_variant 0.21
ethA 4327672 c.-199G>A upstream_gene_variant 0.17
ethA 4328387 c.-914A>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0