TB-Profiler result

Run: ERR245688
Summary

Run ID: ERR245688

Sample name:

Date: 31-03-2023 18:14:58

Number of reads: 11163507

Percentage reads mapped: 99.36

Strain: lineage3.1.1

Drug-resistance: Sensitive

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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
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 0.28
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.99
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.19
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764725 p.Phe452Leu missense_variant 0.16
rpoC 767305 p.Tyr1312* stop_gained 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778899 p.Gly3Arg missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417233 c.115C>T synonymous_variant 0.18
atpE 1461019 c.-26C>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.18
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918069 p.Thr44Pro missense_variant 0.39
ndh 2102891 p.Phe51Ser missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.25
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 0.22
eis 2714569 p.Ala255Gly missense_variant 0.23
eis 2715586 c.-254G>C upstream_gene_variant 0.42
ahpC 2725954 c.-239C>T upstream_gene_variant 0.23
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746186 c.1413G>C synonymous_variant 0.23
pepQ 2859974 p.Ala149Pro missense_variant 0.17
Rv2752c 3064741 p.Gly484Ala missense_variant 0.34
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449673 p.Tyr390* stop_gained 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475280 p.Val425Gly missense_variant 0.24
fbiB 3641955 p.Gly141Arg missense_variant 0.3
fbiB 3642734 c.1200G>C synonymous_variant 0.2
alr 3841504 c.-84C>G upstream_gene_variant 0.2
ddn 3987013 p.Gly57Ala missense_variant 0.25
clpC1 4038857 c.1848C>A synonymous_variant 0.15
clpC1 4039932 p.Gly258Val missense_variant 0.21
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241056 c.1194C>G synonymous_variant 0.24
embC 4241128 c.1266G>C synonymous_variant 0.21
embC 4241429 p.Phe523Val missense_variant 0.4
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 0.99
embC 4242476 p.Pro872Ala missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.38
embA 4244375 c.1143C>G synonymous_variant 0.25
ubiA 4269529 p.Ala102Gly missense_variant 0.22
ethA 4327672 c.-199G>A upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0