TB-Profiler result

Run: ERR4817479
Summary

Run ID: ERR4817479

Sample name:

Date: 01-04-2023 15:00:55

Number of reads: 1125320

Percentage reads mapped: 76.42

Strain: lineage4.1.3

Drug-resistance: Other

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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 1.0
lineage4.1.3 Euro-American T;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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.98 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
gyrB 7235 p.Asn666Asp missense_variant 0.13
gyrA 7249 c.-53T>A upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7667 c.366C>T synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9557 c.2256G>C synonymous_variant 1.0
fgd1 491231 p.Phe150Ser missense_variant 0.1
ccsA 620641 p.Ala251Ser missense_variant 0.18
rpoB 760809 c.1005delC frameshift_variant 0.13
rpoB 761118 p.Asn438Tyr missense_variant 0.12
rpoB 761700 p.Ala632Ser missense_variant 0.12
rpoB 763216 p.Ala1137Val missense_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765696 p.Glu776Gly missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777601 p.Asp294His missense_variant 0.11
mmpL5 777603 p.Gln293Arg missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781407 c.-153C>T upstream_gene_variant 0.22
rpsL 781421 c.-139C>A upstream_gene_variant 1.0
fbiC 1304610 c.1680C>T synonymous_variant 1.0
embR 1416819 p.Lys177Glu missense_variant 0.12
embR 1416897 p.Asp151Asn missense_variant 0.15
embR 1417263 p.Pro29Ala missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471790 n.-56T>C upstream_gene_variant 0.14
rrs 1472498 n.653C>G non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.98
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.98
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.99
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.99
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.99
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.99
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.99
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.97
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.98
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.96
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.75
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.96
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.98
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.98
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.98
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.99
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.99
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.96
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.89
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.89
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.29
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.29
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.29
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.29
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.29
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.67
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.67
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.67
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.57
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.62
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.75
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.62
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.75
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.8
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.89
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.9
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.91
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 1.0
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 1.0
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 1.0
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 1.0
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 1.0
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 1.0
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 1.0
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 1.0
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 1.0
inhA 1674272 p.His24Arg missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154257 p.Leu619Ile missense_variant 0.11
PPE35 2170328 c.285C>T synonymous_variant 0.13
PPE35 2170337 c.276G>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518299 p.Gly62Val missense_variant 0.12
eis 2714380 p.Ser318Phe missense_variant 0.12
Rv2752c 3064546 p.Pro549Leu missense_variant 0.14
thyA 3074141 p.Gln111* stop_gained 0.15
thyA 3074237 p.Ile79Val missense_variant 0.12
thyA 3074452 p.Leu7Pro missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086984 c.165G>C synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474351 c.345C>T synonymous_variant 0.13
clpC1 4038430 p.Leu759Met missense_variant 0.11
clpC1 4039659 p.Glu349Gly missense_variant 0.14
clpC1 4040502 p.Gly68Asp missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245450 c.2218C>T synonymous_variant 0.12
aftB 4267743 p.Arg365Gln missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0