TB-Profiler result

Run: ERR2513306
Summary

Run ID: ERR2513306

Sample name:

Date: 31-03-2023 19:35:31

Number of reads: 779221

Percentage reads mapped: 99.65

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 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.99
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
gyrA 9384 p.Arg695Gly missense_variant 0.11
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575267 c.-81G>A upstream_gene_variant 0.12
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575842 c.495G>A synonymous_variant 0.13
ccsA 620157 c.267G>C synonymous_variant 0.1
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762225 p.Glu807Gln missense_variant 0.13
rpoB 762373 p.Pro856Gln missense_variant 0.14
rpoC 762518 c.-852C>T upstream_gene_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765782 p.Ser805Thr missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776045 c.2436G>A synonymous_variant 0.13
mmpS5 778842 p.Gly22Ser missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303133 p.Ala68Val missense_variant 0.12
fbiC 1305373 p.Thr815Ala missense_variant 0.12
Rv1258c 1407143 c.198C>T synonymous_variant 0.22
Rv1258c 1407410 c.-70C>A upstream_gene_variant 0.12
Rv1258c 1407509 c.-169C>T upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471781 n.-65G>A upstream_gene_variant 1.0
rrl 1475602 n.1945G>A non_coding_transcript_exon_variant 1.0
inhA 1674435 c.234G>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156368 c.-257G>T upstream_gene_variant 0.11
PPE35 2168160 p.Glu818Val missense_variant 0.11
PPE35 2168296 p.Glu773* stop_gained 0.12
PPE35 2169570 p.Ser348Asn missense_variant 0.12
PPE35 2169573 p.Phe347Tyr missense_variant 0.12
PPE35 2169578 c.1035T>C synonymous_variant 0.14
PPE35 2170147 p.Ser156Ala missense_variant 0.17
PPE35 2170157 p.Ala152Ser missense_variant 0.13
PPE35 2170298 c.315A>G synonymous_variant 0.12
PPE35 2170363 p.Glu84Lys missense_variant 0.2
PPE35 2170392 p.Gly74Ala missense_variant 0.2
PPE35 2170400 c.213G>C synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.12
pncA 2290057 c.-816G>T upstream_gene_variant 0.15
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518234 p.Glu40Asp missense_variant 0.2
kasA 2519356 c.1242G>A synonymous_variant 0.12
ahpC 2726338 p.Val49Gly missense_variant 0.24
ahpC 2726350 p.Trp53Leu missense_variant 0.18
folC 2746866 p.Leu245Met missense_variant 0.14
pepQ 2859756 p.Asp221Glu missense_variant 0.11
pepQ 2859976 c.441_442delCG frameshift_variant 0.14
pepQ 2860042 p.Gly126Glu missense_variant 0.13
Rv2752c 3064917 c.1275C>T synonymous_variant 0.11
Rv2752c 3067117 c.-926C>G upstream_gene_variant 0.12
thyX 3067481 c.465C>A synonymous_variant 0.17
thyA 3073713 c.759G>A synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087160 p.Ser114* stop_gained 0.11
Rv3083 3448667 p.Ser55Leu missense_variant 0.2
Rv3083 3448787 p.Asp95Val missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474078 c.72G>A synonymous_variant 0.2
fprA 3474137 p.Thr44Asn missense_variant 0.12
fprA 3474144 p.Trp46Cys missense_variant 0.11
Rv3236c 3612845 p.Pro91Leu missense_variant 0.12
Rv3236c 3612910 p.Leu69Phe missense_variant 0.15
alr 3840919 p.Gly168* stop_gained 0.13
alr 3841612 c.-193_-192insC upstream_gene_variant 0.14
ddn 3986703 c.-141T>C upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243488 p.Gly86Cys missense_variant 0.12
embA 4244048 c.816C>T synonymous_variant 0.12
embA 4245441 p.Asp737Asn missense_variant 0.17
embB 4246675 c.162G>T synonymous_variant 0.22
aftB 4267159 p.Thr560Ser missense_variant 0.11
ethA 4326483 p.Arg331Cys missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0