TB-Profiler result

Run: ERR4821262

Summary

Run ID: ERR4821262

Sample name:

Date: 01-04-2023 17:09:13

Number of reads: 511715

Percentage reads mapped: 99.48

Strain: lineage4.1.1.3

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
lineage4.1.1 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
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 9628 p.Ala776Val missense_variant 0.17
mshA 575581 c.234C>T synonymous_variant 0.5
mshA 576641 p.Asn432Asp missense_variant 0.33
mshA 576670 c.1323T>C synonymous_variant 0.29
ccsA 620272 p.Val128Leu missense_variant 0.33
rpoB 762874 p.Tyr1023Cys missense_variant 0.11
rpoC 762926 c.-444C>T upstream_gene_variant 0.12
rpoB 762927 p.Gly1041Arg missense_variant 0.13
rpoB 763014 p.Met1070Val missense_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765788 p.Ala807Pro missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777738 p.Ala248Asp missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304476 p.Ala516Thr missense_variant 0.4
Rv1258c 1406258 c.1083G>T synonymous_variant 0.12
embR 1416694 c.654C>A synonymous_variant 0.15
embR 1417176 p.Ala58Thr missense_variant 0.18
embR 1417371 c.-24A>T upstream_gene_variant 0.11
atpE 1461146 c.102G>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473733 n.76C>A non_coding_transcript_exon_variant 0.25
fabG1 1673533 p.Ala32Thr missense_variant 0.14
inhA 1674702 c.501G>T synonymous_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102427 p.Ser206Pro missense_variant 1.0
ndh 2102653 p.His130Glu missense_variant 0.17
ndh 2102668 c.375T>C synonymous_variant 0.17
ndh 2102671 c.372T>C synonymous_variant 0.17
ndh 2102875 p.Tyr56Phe missense_variant 0.18
katG 2156066 p.Ala16Ser missense_variant 0.12
PPE35 2167700 c.2913C>T synonymous_variant 0.18
PPE35 2168385 p.Glu743Gly missense_variant 0.22
PPE35 2168751 p.Ser621Asn missense_variant 0.13
PPE35 2169551 c.1062C>T synonymous_variant 0.14
PPE35 2170115 c.498G>A synonymous_variant 0.22
Rv1979c 2222060 p.Phe369Leu missense_variant 0.15
Rv1979c 2222610 c.555C>T synonymous_variant 0.22
Rv1979c 2222668 p.Ser166Leu missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289989 c.-748C>T upstream_gene_variant 0.14
kasA 2517977 c.-138C>T upstream_gene_variant 0.12
kasA 2518313 p.Pro67Ser missense_variant 0.33
eis 2715432 c.-100C>T upstream_gene_variant 0.2
folC 2746984 c.615C>A synonymous_variant 0.33
folC 2747094 p.Asp169Asn missense_variant 0.22
ribD 2986869 p.Asp11Asn missense_variant 0.17
Rv2752c 3064554 c.1638C>T synonymous_variant 0.33
Rv2752c 3065950 p.His81Arg missense_variant 0.17
Rv2752c 3067181 c.-990G>T upstream_gene_variant 0.33
ald 3086735 c.-85C>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339181 p.Ala22Thr missense_variant 0.33
Rv3083 3449058 c.555C>T synonymous_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474408 c.402A>G synonymous_variant 0.1
whiB7 3568543 p.Cys46Phe missense_variant 0.17
rpoA 3877491 c.1016delA frameshift_variant 0.13
rpoA 3877976 p.Val178Met missense_variant 0.18
clpC1 4040705 c.-1G>A upstream_gene_variant 0.22
embC 4240517 p.Asp219His missense_variant 0.22
embC 4240539 p.Pro226Leu missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244082 c.854delC frameshift_variant 0.12
embA 4244603 c.1371G>A synonymous_variant 0.2
embA 4245313 p.Ala694Glu missense_variant 0.18
embB 4247798 p.Thr429Ala missense_variant 0.11
embB 4248955 c.2442C>T synonymous_variant 0.22
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249688 p.Arg1059Cys missense_variant 0.25
ethR 4327895 p.Ser116Leu missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0