TB-Profiler result

Run: ERR2514771

Summary

Run ID: ERR2514771

Sample name:

Date: 31-03-2023 20:33:09

Number of reads: 636793

Percentage reads mapped: 97.55

Strain: lineage4.8.2

Drug-resistance: RR-TB


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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
lineage4.8.2 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rpoB 761140 p.His445Leu missense_variant 0.14 rifampicin
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 5701 c.466dupC frameshift_variant 0.11
gyrA 6955 c.-347G>A upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8135 c.834C>T synonymous_variant 1.0
gyrA 8558 c.1257C>A synonymous_variant 0.1
fgd1 491696 p.Leu305Pro missense_variant 0.13
rpoB 759620 c.-187A>C upstream_gene_variant 0.29
rpoB 760638 p.Gly278Cys missense_variant 0.12
rpoB 760973 c.1167G>C synonymous_variant 0.14
rpoB 760982 c.1176G>C synonymous_variant 0.15
rpoB 760988 c.1182C>G synonymous_variant 0.17
rpoB 760991 c.1185G>C synonymous_variant 0.17
rpoB 760997 c.1191G>C synonymous_variant 0.18
rpoB 761006 c.1200C>G synonymous_variant 0.17
rpoB 761014 p.Val403Ala missense_variant 0.17
rpoB 761021 c.1215G>C synonymous_variant 0.17
rpoB 761027 c.1221A>C synonymous_variant 0.15
rpoB 761034 p.Thr410Ser missense_variant 0.13
rpoB 761051 c.1245G>C synonymous_variant 0.12
rpoB 761058 p.Val418Asn missense_variant 0.12
rpoB 761064 p.Ala420Thr missense_variant 0.12
rpoC 764459 p.Glu364* stop_gained 0.11
rpoC 766716 p.Ala1116Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776699 c.1782C>A synonymous_variant 0.1
mmpL5 776891 p.Gln530His missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416674 p.Leu225Pro missense_variant 0.13
atpE 1460872 c.-173G>T upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475933 n.2276C>T non_coding_transcript_exon_variant 0.18
rrl 1476287 n.2630A>G non_coding_transcript_exon_variant 0.15
rpsA 1834335 c.795delC frameshift_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168258 c.2355G>A synonymous_variant 0.14
PPE35 2170484 c.129C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289913 c.-672T>A upstream_gene_variant 0.13
kasA 2519062 c.948T>G synonymous_variant 0.1
ahpC 2725972 c.-221A>G upstream_gene_variant 0.11
ribD 2986773 c.-66G>T upstream_gene_variant 0.1
ald 3086987 p.Gln56His missense_variant 0.12
ald 3086997 p.Thr60Gly missense_variant 0.13
whiB7 3568782 c.-106_-104delACA upstream_gene_variant 0.12
whiB7 3568788 c.-109G>T upstream_gene_variant 0.12
whiB7 3568789 c.-110A>C upstream_gene_variant 0.18
whiB7 3568873 c.-194G>T upstream_gene_variant 0.12
Rv3236c 3612863 p.Ser85Ile missense_variant 0.13
fbiA 3641477 p.Asp312Val missense_variant 0.11
fbiB 3641640 p.Ala36Thr missense_variant 0.1
rpoA 3877713 p.Lys265Asn missense_variant 0.11
clpC1 4039729 p.Asp326Asn missense_variant 0.82
clpC1 4039730 c.975C>G synonymous_variant 0.18
clpC1 4039782 p.Leu308Gln missense_variant 0.1
embC 4241979 p.Ser706Phe missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245848 c.-666C>A upstream_gene_variant 0.15
aftB 4268584 p.Ala85Thr missense_variant 0.15
ethA 4326638 p.Arg279Gln missense_variant 0.11
ethR 4328102 c.555_560delGTCATT disruptive_inframe_deletion 0.17
ethR 4328111 p.Ala188Gly missense_variant 0.17
ethR 4328113 c.565_566insAATGAC stop_gained&disruptive_inframe_insertion 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407968 c.235T>C synonymous_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0