TB-Profiler result

Run: ERR2510765

Summary

Run ID: ERR2510765

Sample name:

Date: 31-03-2023 18:55:40

Number of reads: 613423

Percentage reads mapped: 96.87

Strain: lineage4.8

Drug-resistance: Pre-XDR-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
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
gyrB 6735 p.Asn499Thr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781821 p.Lys88Gln missense_variant 1.0 streptomycin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.19 streptomycin
katG 2154352 p.Leu587Pro missense_variant 0.12 isoniazid
katG 2155167 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289038 p.Trp68* stop_gained 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
embB 4247729 p.Gly406Cys missense_variant 1.0 ethambutol
ethA 4326969 c.504delC frameshift_variant 1.0 ethionamide
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 7670 c.369A>T synonymous_variant 0.1
gyrA 8816 c.1515C>T synonymous_variant 0.12
fgd1 490684 c.-99G>A upstream_gene_variant 0.17
fgd1 491077 p.Asn99Tyr missense_variant 0.17
mshA 575965 c.618C>T synonymous_variant 0.12
ccsA 620843 p.His318Leu missense_variant 0.11
rpoB 759955 p.Val50Gly missense_variant 1.0
rpoC 764487 p.Met373Thr missense_variant 0.11
rpoC 765713 p.Thr782Ala missense_variant 1.0
rpoC 766691 p.Gly1108Arg missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777602 p.Gln293His missense_variant 0.12
mmpL5 779298 c.-818G>A upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304443 p.Ala505Ser missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.13
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.13
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.33
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.35
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.19
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.17
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.17
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.17
rrs 1472842 n.997G>T non_coding_transcript_exon_variant 0.11
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.14
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.14
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.14
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.14
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.17
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.17
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.17
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.31
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.43
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.43
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.33
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.12
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.15
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.14
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.14
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.14
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.12
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.12
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.13
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.12
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.24
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.3
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.14
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.11
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475729 n.2072C>G non_coding_transcript_exon_variant 0.18
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.2
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.25
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.25
inhA 1674855 c.654C>T synonymous_variant 0.15
rpsA 1834737 p.Glu399Gly missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154513 c.1599G>T synonymous_variant 0.12
katG 2155635 c.477C>T synonymous_variant 0.11
katG 2156420 c.-309A>G upstream_gene_variant 0.11
PPE35 2168228 c.2385C>T synonymous_variant 0.12
PPE35 2170636 c.-24G>A upstream_gene_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289698 c.-458delT upstream_gene_variant 0.11
kasA 2519184 p.Leu357Pro missense_variant 0.14
kasA 2519208 p.Gly365Asp missense_variant 0.14
folC 2746468 c.1131G>T synonymous_variant 0.17
Rv2752c 3064976 p.Asn406Asp missense_variant 0.17
ald 3087130 p.Thr104Asn missense_variant 0.11
ald 3087251 c.434dupG frameshift_variant 1.0
fbiD 3339178 p.Ala21Ser missense_variant 0.11
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612084 p.Gly345Ser missense_variant 0.11
fbiA 3640901 p.Gln120Arg missense_variant 1.0
fbiB 3642178 p.Ala215Val missense_variant 0.2
ddn 3986904 p.Met21Val missense_variant 0.11
clpC1 4038967 p.Ile580Phe missense_variant 0.1
clpC1 4040129 c.576C>T synonymous_variant 0.15
embC 4239711 c.-152C>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246006 p.Leu925Pro missense_variant 0.11
embA 4246057 p.Val942Asp missense_variant 0.12
embB 4246584 p.Arg24Pro missense_variant 0.2
embB 4246941 p.Pro143Arg missense_variant 0.13
embB 4247015 p.Ser168Pro missense_variant 0.11
ubiA 4269578 c.255delC frameshift_variant 0.12
ubiA 4269715 p.Leu40Ser missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0