TB-Profiler result

Run: SRR19428565
Summary

Run ID: SRR19428565

Sample name:

Date: 03-04-2023 21:40:25

Number of reads: 182989

Percentage reads mapped: 99.65

Strain: lineage4.6.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 1.0
lineage4.6.1.1 Euro-American T2-Uganda RD724 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 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491788 p.Gly336Cys missense_variant 0.14
mshA 575998 c.651C>T synonymous_variant 0.12
ccsA 620361 p.Tyr157* stop_gained 0.25
rpoB 760977 p.Glu391* stop_gained 0.25
rpoC 765035 p.Arg556Ser missense_variant 0.12
rpoC 767138 p.Leu1257Met missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776370 p.Gly704Val missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303418 p.Gly163Val missense_variant 0.22
Rv1258c 1406329 p.Thr338Ser missense_variant 0.11
embR 1417151 p.Ser66Leu missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472970 n.1125C>T non_coding_transcript_exon_variant 0.13
rrl 1473770 n.113T>C non_coding_transcript_exon_variant 0.14
rrl 1473773 n.116C>T non_coding_transcript_exon_variant 0.14
rrl 1476144 n.2487T>C non_coding_transcript_exon_variant 0.22
inhA 1674886 p.Gly229Cys missense_variant 0.33
rpsA 1834314 p.Val258Ala missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155836 c.276C>A synonymous_variant 0.17
Rv1979c 2222630 p.Val179Ile missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289303 c.-62T>A upstream_gene_variant 0.25
pncA 2289911 c.-670G>C upstream_gene_variant 0.13
kasA 2519006 p.Ala298Ser missense_variant 0.33
kasA 2519262 p.Asp383Gly missense_variant 0.22
folC 2747081 p.Val173Asp missense_variant 0.33
pepQ 2860264 p.Ala52Val missense_variant 0.18
Rv2752c 3065534 p.Pro220Ser missense_variant 0.22
Rv2752c 3066057 c.135C>T synonymous_variant 0.12
Rv3083 3449822 p.Asn440Ser missense_variant 0.12
Rv3083 3449891 p.Leu463Pro missense_variant 0.15
fprA 3473998 c.-9G>A upstream_gene_variant 1.0
fprA 3473998 c.-10_-9insA upstream_gene_variant 1.0
whiB7 3568451 p.Val77Met missense_variant 0.33
whiB7 3568686 c.-7A>G upstream_gene_variant 1.0
fbiB 3640737 c.-798C>T upstream_gene_variant 0.2
rpoA 3878121 c.387C>T synonymous_variant 0.22
ddn 3986773 c.-71G>A upstream_gene_variant 0.14
panD 4044262 p.Lys7Arg missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267778 c.1059T>A synonymous_variant 0.67
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0