TB-Profiler result

Run: SRR14165120
Summary

Run ID: SRR14165120

Sample name:

Date: 03-04-2023 10:15:34

Number of reads: 1321483

Percentage reads mapped: 99.17

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.17
mshA 576482 p.Val379Leu missense_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767238 p.Asp1290Val missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776760 p.Phe574Ser missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475805 n.2148G>A non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102824 c.219G>A synonymous_variant 0.13
katG 2154597 p.Trp505Cys missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223344 c.-180A>G upstream_gene_variant 0.13
pncA 2289356 c.-115G>A upstream_gene_variant 0.12
pncA 2289676 c.-435T>A upstream_gene_variant 0.15
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726171 c.-22C>A upstream_gene_variant 0.12
pepQ 2859300 c.1119G>T stop_lost&splice_region_variant 0.12
Rv2752c 3064776 p.Phe472Leu missense_variant 0.11
Rv2752c 3064779 c.1413C>G synonymous_variant 0.11
Rv2752c 3065453 p.Gln247* stop_gained 0.26
thyA 3074176 p.Arg99Leu missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 0.93
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877686 p.Glu274Asp missense_variant 0.11
rpoA 3877703 p.Val269Met missense_variant 0.12
ddn 3986833 c.-11G>T upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
aftB 4267211 c.1626C>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0