TB-Profiler result

Run: ERR216985
Summary

Run ID: ERR216985

Sample name:

Date: 31-03-2023 15:57:43

Number of reads: 1144425

Percentage reads mapped: 95.34

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 0.96
lineage4.1.2 Euro-American T;H None 0.96
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 8337 c.1036C>T synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576650 p.Asp435Asn missense_variant 0.18
ccsA 620054 p.Ala55Val missense_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 0.99
rpoB 761804 p.Met666Ile missense_variant 0.11
rpoC 762558 c.-812C>A upstream_gene_variant 0.15
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
fbiC 1304159 p.Val410Gly missense_variant 0.29
fbiC 1304773 p.Ala615Ser missense_variant 0.12
Rv1258c 1406802 p.Ala180Glu missense_variant 0.14
embR 1416883 p.Asp155Glu missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.1
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.22
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.11
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.11
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.12
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.12
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102466 p.Ala193Thr missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714182 p.Arg384His missense_variant 0.12
eis 2714781 c.552G>A synonymous_variant 0.4
folC 2746630 c.969C>T synonymous_variant 0.13
ribD 2986704 c.-135G>T upstream_gene_variant 0.12
thyA 3074065 p.Gly136Asp missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474218 p.Ala71Val missense_variant 0.15
fbiB 3642004 p.Arg157Leu missense_variant 0.15
alr 3840281 c.1140C>T synonymous_variant 0.15
alr 3840643 c.778C>T synonymous_variant 0.12
alr 3840959 c.462G>A synonymous_variant 0.12
alr 3840983 c.438C>A synonymous_variant 0.13
clpC1 4038958 p.Gly583Ser missense_variant 0.13
clpC1 4038987 c.1715_1717delGTG disruptive_inframe_deletion 0.14
clpC1 4038997 c.1708T>C synonymous_variant 0.18
clpC1 4039003 p.Asn568Asp missense_variant 0.18
clpC1 4039018 p.Ser563Ala missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
aftB 4268121 p.Thr239Ile missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0