TB-Profiler result

Run: ERR2515154
Summary

Run ID: ERR2515154

Sample name:

Date: 31-03-2023 20:47:00

Number of reads: 423569

Percentage reads mapped: 99.61

Strain: lineage4.1.1.3

Drug-resistance: Other

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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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
pncA 2288721 p.Glu174Gly missense_variant 0.2 pyrazinamide
embB 4247429 p.Met306Leu missense_variant 0.12 ethambutol
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
gyrB 6801 p.Lys521Arg missense_variant 0.12
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 9542 c.2241T>A synonymous_variant 0.12
fgd1 490872 c.92dupG frameshift_variant 0.12
mshA 575596 c.249C>T synonymous_variant 0.14
mshA 576478 c.1134delC frameshift_variant 0.22
rpoB 762619 p.Trp938* stop_gained 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766767 p.His1133Leu missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777198 p.Asn428Ser missense_variant 0.12
mmpL5 777415 p.Ala356Thr missense_variant 0.12
mmpL5 777594 p.Glu296Gly missense_variant 0.13
mmpL5 777726 p.Phe252Ser missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473931 n.274A>G non_coding_transcript_exon_variant 0.13
rrl 1474422 n.765C>G non_coding_transcript_exon_variant 0.2
inhA 1674334 p.Arg45Gly missense_variant 0.1
rpsA 1833396 c.-145delG upstream_gene_variant 0.12
rpsA 1833442 c.-100G>A upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102128 c.915G>T synonymous_variant 0.12
Rv1979c 2222826 c.338delT frameshift_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289314 c.-73T>C upstream_gene_variant 0.11
folC 2746999 c.600T>C synonymous_variant 0.11
folC 2747156 p.Ala148Glu missense_variant 0.11
folC 2747627 c.-29C>A upstream_gene_variant 0.13
Rv2752c 3066096 c.96G>T synonymous_variant 0.12
thyA 3073723 p.Asn250Thr missense_variant 0.11
thyA 3074612 c.-141G>T upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087077 c.258A>G synonymous_variant 0.12
fbiD 3339289 p.Ser58Pro missense_variant 0.17
Rv3083 3449279 p.Arg259Gln missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474278 p.Gly91Asp missense_variant 0.11
fprA 3475013 p.Asp336Gly missense_variant 0.2
Rv3236c 3612491 p.Leu209Ser missense_variant 0.29
fbiA 3640598 p.Val19Ala missense_variant 0.14
fbiA 3640858 p.Asp106Tyr missense_variant 0.12
fbiA 3641403 p.Cys287* stop_gained 0.12
rpoA 3878484 c.24C>A synonymous_variant 0.22
embC 4241077 c.1215C>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244343 p.Ala371Ser missense_variant 0.15
embA 4246009 p.Arg926Gln missense_variant 0.11
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4266969 p.Pro623Gln missense_variant 0.14
aftB 4267933 p.Ala302Pro missense_variant 0.11
ethA 4327019 p.Ala152Val missense_variant 0.95
ethA 4327383 p.Ser31Gly missense_variant 0.14
ethA 4327395 p.Cys27Arg missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0