TB-Profiler result

Run: SRR6855900
Summary

Run ID: SRR6855900

Sample name:

Date: 04-04-2023 17:49:27

Number of reads: 361294

Percentage reads mapped: 99.61

Strain: lineage4.1.2

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
lineage4.1.2 Euro-American T;H None 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 2288829 p.Cys138Tyr missense_variant 0.13 pyrazinamide
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 7683 p.Arg128Gly missense_variant 0.11
gyrA 7809 p.Phe170Leu missense_variant 0.11
gyrA 8955 p.Asp552Asn missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575198 c.-150_-149insGT upstream_gene_variant 0.1
mshA 576174 p.Pro276Leu missense_variant 0.1
ccsA 620374 p.Pro162Thr missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800700 c.-109C>T upstream_gene_variant 0.11
rplC 801186 c.378C>T synonymous_variant 1.0
Rv1258c 1406729 c.612G>A synonymous_variant 0.15
embR 1416381 p.Ala323Thr missense_variant 0.12
embR 1417140 p.Ala70Ser missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 0.9
rrs 1471690 n.-156G>A upstream_gene_variant 0.1
rrs 1473099 n.1254T>C non_coding_transcript_exon_variant 0.1
rrl 1474828 n.1171G>A non_coding_transcript_exon_variant 0.11
fabG1 1673249 c.-191C>T upstream_gene_variant 1.0
fabG1 1674103 p.Ser222Gly missense_variant 0.12
inhA 1674410 p.His70Arg missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747022 p.Val193Ile missense_variant 1.0
pepQ 2859894 p.Glu175Asp missense_variant 0.12
Rv2752c 3064667 p.Arg509Cys missense_variant 0.12
Rv2752c 3064847 p.Val449Phe missense_variant 0.12
Rv2752c 3064942 p.Gln417Arg missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087553 p.Lys245Met missense_variant 0.14
fbiD 3339032 c.-86C>T upstream_gene_variant 0.11
Rv3083 3448894 p.Tyr131Asp missense_variant 1.0
Rv3083 3449081 p.Val193Asp missense_variant 0.12
Rv3083 3449642 p.Asn380Ser missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.94
fprA 3474878 p.Arg291Pro missense_variant 0.15
fprA 3474887 p.Leu294Gln missense_variant 0.14
fprA 3475360 c.1356dupG frameshift_variant 0.15
fbiA 3641164 p.Ile208Val missense_variant 1.0
ddn 3986802 c.-42G>C upstream_gene_variant 0.11
ddn 3987025 p.Val61Gly missense_variant 1.0
clpC1 4039647 p.Glu353Gly missense_variant 0.18
clpC1 4040149 p.Lys186Glu missense_variant 0.11
panD 4044215 p.Val23Ile missense_variant 0.12
embC 4240681 c.819G>A synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243342 p.Asn37Ser missense_variant 0.18
embA 4243382 c.150C>T synonymous_variant 0.17
embB 4246653 p.Leu47Pro missense_variant 0.13
aftB 4267717 p.Ala374Pro missense_variant 0.14
aftB 4267908 p.Ala310Val missense_variant 0.13
aftB 4268212 p.Arg209Cys missense_variant 0.11
aftB 4268861 c.-25T>C upstream_gene_variant 1.0
ubiA 4269073 p.Pro254Leu missense_variant 0.12
ubiA 4269586 p.Glu83Gly missense_variant 0.13
ethA 4326029 p.Lys482Ile missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0