TB-Profiler result

Run: ERR11049143
Summary

Run ID: ERR11049143

Sample name:

Date: 31-03-2023 12:36:12

Number of reads: 3697490

Percentage reads mapped: 97.95

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 0.99
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.17
mshA 576482 p.Val379Leu missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 0.98
rpoC 764560 c.1191T>C synonymous_variant 0.13
rpoC 764566 c.1197C>G synonymous_variant 0.13
rpoC 764575 c.1206T>G synonymous_variant 0.14
rpoC 764581 c.1212T>C synonymous_variant 0.13
rpoC 764593 c.1224C>T synonymous_variant 0.12
rpoC 764611 c.1242G>T synonymous_variant 0.13
rpoC 764650 c.1281G>C synonymous_variant 0.11
rpoC 764651 c.1282_1284delTCGinsAGC synonymous_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 0.99
rpoC 765541 c.2172C>G synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303858 p.Gly310Arg missense_variant 0.92
Rv1258c 1407079 c.261delC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169041 c.1572G>A synonymous_variant 0.3
PPE35 2169044 c.1569G>C synonymous_variant 0.5
PPE35 2169047 p.Ile522Val missense_variant 0.47
PPE35 2169053 c.1560T>C synonymous_variant 1.0
PPE35 2169056 c.1557A>G synonymous_variant 0.47
PPE35 2169059 c.1554G>A synonymous_variant 0.53
PPE35 2169063 p.Met517Thr missense_variant 1.0
PPE35 2169065 p.Ala516Ile missense_variant 0.53
PPE35 2169068 c.1545G>T synonymous_variant 0.53
PPE35 2169071 c.1542A>G synonymous_variant 0.43
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2725938 c.-255G>T upstream_gene_variant 1.0
ahpC 2725939 c.-254C>T upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.59
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878613 c.-106A>C upstream_gene_variant 0.29
rpoA 3878618 c.-111A>C upstream_gene_variant 0.23
rpoA 3878637 c.-130G>C upstream_gene_variant 0.22
rpoA 3878641 c.-134C>G upstream_gene_variant 0.28
embC 4240409 p.Pro183Ala missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.98
embB 4246584 p.Arg24Pro missense_variant 0.43
whiB6 4338595 c.-75delG upstream_gene_variant 1.0