TB-Profiler result

Run: ERR2514277
Summary

Run ID: ERR2514277

Sample name:

Date: 31-03-2023 20:14:11

Number of reads: 700292

Percentage reads mapped: 98.68

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
gyrB 6932 p.Gln565Lys missense_variant 0.29
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 9632 c.2331C>T synonymous_variant 0.2
fgd1 491341 p.Arg187Gly missense_variant 0.14
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 0.92
rpoB 759615 c.-192A>C upstream_gene_variant 0.29
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760835 c.1029C>T synonymous_variant 0.29
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778646 p.Pro87Arg missense_variant 0.18
mmpR5 779294 p.Ala102Asp missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800988 c.180C>A synonymous_variant 0.21
fbiC 1304122 p.Tyr398His missense_variant 0.12
fbiC 1304867 p.Gly646Glu missense_variant 0.2
Rv1258c 1407148 p.Ala65Thr missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.67
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.67
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.67
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.57
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.57
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.57
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.57
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153938 p.Val725Gly missense_variant 0.13
PPE35 2169044 c.1569G>C synonymous_variant 1.0
PPE35 2169047 p.Ile522Val missense_variant 1.0
PPE35 2169053 c.1560T>C synonymous_variant 1.0
PPE35 2169056 c.1557A>G synonymous_variant 1.0
PPE35 2169063 p.Met517Thr missense_variant 1.0
PPE35 2169066 p.Ala516Val missense_variant 1.0
PPE35 2169071 c.1542A>G synonymous_variant 0.5
PPE35 2170443 p.Trp57Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517950 c.-165C>G upstream_gene_variant 0.1
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518771 c.659delA frameshift_variant 0.25
eis 2714266 p.Leu356Pro missense_variant 0.1
eis 2715465 c.-133G>T upstream_gene_variant 0.12
eis 2715469 c.-137T>C upstream_gene_variant 0.13
eis 2715473 c.-141A>G upstream_gene_variant 0.13
folC 2746558 c.1041G>T synonymous_variant 0.18
pepQ 2859820 p.Ser200* stop_gained 0.13
ribD 2987471 c.633G>A synonymous_variant 0.13
Rv2752c 3064898 p.Val432Ile missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641900 c.366G>T synonymous_variant 0.14
clpC1 4038965 c.1740T>C synonymous_variant 0.15
clpC1 4038971 c.1734T>C synonymous_variant 0.13
clpC1 4038974 c.1731T>C synonymous_variant 0.13
clpC1 4038989 c.1716T>C synonymous_variant 0.12
clpC1 4038997 c.1708T>C synonymous_variant 0.12
clpC1 4039004 c.1701C>G synonymous_variant 0.13
clpC1 4039016 c.1689C>G synonymous_variant 0.14
clpC1 4039022 c.1683A>G synonymous_variant 0.12
clpC1 4039093 p.Gly538Arg missense_variant 0.15
clpC1 4039508 c.1197G>C synonymous_variant 0.13
embC 4240655 p.Ala265Pro missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4246033 p.Pro934Leu missense_variant 0.18
aftB 4267623 c.1213delT frameshift_variant 0.17
aftB 4268924 c.-88C>A upstream_gene_variant 0.12
whiB6 4338419 p.Thr35Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0