TB-Profiler result

Run: ERR245671
Summary

Run ID: ERR245671

Sample name:

Date: 31-03-2023 18:13:33

Number of reads: 14338907

Percentage reads mapped: 99.34

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 0.24
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.27
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.19
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 762249 p.Leu815Val missense_variant 0.18
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.28
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764725 p.Phe452Leu missense_variant 0.19
rpoC 767305 p.Tyr1312* stop_gained 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800997 p.Asn63Lys missense_variant 0.18
embR 1417136 p.Ser71Ile missense_variant 0.22
atpE 1461019 c.-26C>A upstream_gene_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.17
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.17
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.18
inhA 1674892 p.Asn231Asp missense_variant 0.25
rpsA 1833712 p.Tyr57* stop_gained 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167871 c.2742G>C synonymous_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.23
PPE35 2170461 p.Gly51Glu missense_variant 1.0
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 0.23
eis 2715586 c.-254G>C upstream_gene_variant 0.31
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746186 c.1413G>C synonymous_variant 0.17
pepQ 2859787 p.Val211Ala missense_variant 1.0
pepQ 2859974 p.Ala149Pro missense_variant 0.18
Rv2752c 3064741 p.Gly484Ala missense_variant 0.23
thyX 3067965 c.-20C>G upstream_gene_variant 0.29
thyA 3073817 p.Gln219Glu missense_variant 0.28
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611982 p.Ala379Pro missense_variant 0.42
fbiB 3641955 p.Gly141Arg missense_variant 0.26
ddn 3987013 p.Gly57Ala missense_variant 0.19
clpC1 4038857 c.1848C>A synonymous_variant 0.16
clpC1 4039932 p.Gly258Val missense_variant 0.26
embC 4239870 p.Thr3Asn missense_variant 0.18
embC 4241056 c.1194C>G synonymous_variant 0.29
embC 4241429 p.Phe523Val missense_variant 0.33
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.31
embA 4244375 c.1143C>G synonymous_variant 0.2
embB 4247041 c.528C>T synonymous_variant 0.2
ubiA 4269529 p.Ala102Gly missense_variant 0.17
ethA 4327672 c.-199G>A upstream_gene_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0