TB-Profiler result

Run: ERR9901852

Summary

Run ID: ERR9901852

Sample name:

Date: 02-04-2023 13:33:43

Number of reads: 696872

Percentage reads mapped: 99.51

Strain: lineage4.8

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
lineage4.8 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
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 9337 p.Gln679Arg missense_variant 0.12
fgd1 490705 c.-77delG upstream_gene_variant 0.12
rpoB 760341 p.Val179Met missense_variant 0.15
rpoB 761283 p.Ser493Thr missense_variant 0.15
rpoC 765430 c.2061G>A synonymous_variant 0.13
rpoC 767036 p.Ala1223Ser missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776127 p.Cys785Tyr missense_variant 0.12
mmpL5 776877 c.1603delC frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781731 p.Thr58Ser missense_variant 0.11
rplC 801186 c.378C>T synonymous_variant 0.14
Rv1258c 1407071 c.270C>T synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473126 n.1281A>G non_coding_transcript_exon_variant 0.92
rrl 1473976 n.319T>A non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476205 n.2548A>C non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154294 c.1818C>T synonymous_variant 0.11
katG 2154577 p.Gly512Ala missense_variant 0.1
katG 2155916 p.Ala66Thr missense_variant 0.2
PPE35 2168207 p.Asp802Glu missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.17
Rv1979c 2222058 c.1107C>T synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290055 c.-814A>T upstream_gene_variant 0.12
kasA 2518103 c.-12G>A upstream_gene_variant 0.12
kasA 2518729 c.618delC frameshift_variant 0.11
eis 2715040 p.Arg98His missense_variant 0.11
folC 2746320 p.Pro427Ser missense_variant 0.11
ribD 2987584 p.Gly249Val missense_variant 0.11
Rv2752c 3064573 p.Trp540Ser missense_variant 0.11
thyX 3067998 c.-53C>T upstream_gene_variant 0.1
Rv3083 3448424 c.-80C>A upstream_gene_variant 0.12
fprA 3474697 p.Asp231Asn missense_variant 0.12
fprA 3475006 p.Phe334Ile missense_variant 0.18
whiB7 3568510 p.Leu57Pro missense_variant 0.14
Rv3236c 3611972 p.Val382Ala missense_variant 0.13
Rv3236c 3612423 p.Val232Met missense_variant 0.13
alr 3840764 c.657G>C synonymous_variant 1.0
panD 4044251 p.His11Asn missense_variant 0.11
panD 4044435 c.-154C>A upstream_gene_variant 0.11
panD 4044438 c.-159_-158delTG upstream_gene_variant 0.12
panD 4044473 c.-192G>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247139 p.Arg209Leu missense_variant 0.11
aftB 4268378 p.Trp153* stop_gained 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407616 p.Leu196Ser missense_variant 0.1
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0