TB-Profiler result

Run: ERR4812866
Summary

Run ID: ERR4812866

Sample name:

Date: 01-04-2023 12:23:23

Number of reads: 274372

Percentage reads mapped: 99.39

Strain: lineage4

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247469 p.Tyr319Ser missense_variant 1.0 ethambutol
gid 4407952 p.Pro84Leu missense_variant 1.0 streptomycin
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 6928 c.-374G>A upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
rpoB 759923 c.117C>T synonymous_variant 0.11
rpoB 760327 p.Val174Ala missense_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778894 c.-414T>C upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303679 p.Arg250Gln missense_variant 0.33
Rv1258c 1406521 p.Gly274Arg missense_variant 0.18
atpE 1461138 p.Gly32Ser missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473005 n.1160C>A non_coding_transcript_exon_variant 0.17
rpsA 1833371 c.-171G>A upstream_gene_variant 0.5
rpsA 1834339 p.Asp266Glu missense_variant 0.15
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 1.0
ndh 2102050 c.993T>G synonymous_variant 0.5
katG 2155213 p.Trp300Leu missense_variant 0.18
PPE35 2168998 p.Ile539Val missense_variant 0.88
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518412 p.Ser100Gly missense_variant 0.15
folC 2746749 p.Gly284Trp missense_variant 1.0
pepQ 2859369 c.1050A>G synonymous_variant 0.22
thyX 3068146 c.-201T>C upstream_gene_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473957 c.-50C>T upstream_gene_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568558 p.Thr41Ile missense_variant 0.29
whiB7 3568720 c.-41C>T upstream_gene_variant 0.11
alr 3840719 c.702A>G synonymous_variant 0.29
alr 3841468 c.-48C>T upstream_gene_variant 0.14
ddn 3987275 c.432C>T synonymous_variant 0.15
embC 4241921 p.Gly687Trp missense_variant 0.25
ethA 4327267 p.Trp69Cys missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408388 c.-186C>A upstream_gene_variant 0.5