TB-Profiler result

Run: ERR4818926
Summary

Run ID: ERR4818926

Sample name:

Date: 01-04-2023 15:49:57

Number of reads: 4238922

Percentage reads mapped: 96.99

Strain: lineage4.6.2.2

Drug-resistance: HR-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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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 0.54 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.1
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.1
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.12
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.11
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.1
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.17
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.21
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.22
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.22
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.17
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.3
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.42
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.42
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.61
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.65
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.73
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.71
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.56
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.21
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.69
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.76
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.76
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.21
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.19
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.46
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.14
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.43
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.56
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.56
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.62
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.11
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.62
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.66
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.4
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.17
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.25
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.18
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.12
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.15
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.24
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.21
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.21
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.21
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.19
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.11
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.11
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.11
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.14
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.12
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.1
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.1
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.22
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.2
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.22
rrl 1474275 n.618T>C non_coding_transcript_exon_variant 0.22
rrl 1474278 n.621G>C non_coding_transcript_exon_variant 0.33
rrl 1474596 n.939T>C non_coding_transcript_exon_variant 0.67
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 1.0
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.75
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.14
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.12
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.12
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.17
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.17
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.17
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.34
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.32
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.29
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.31
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.21
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.17
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.21
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155389 c.723C>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067474 p.Pro158Ala missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612910 p.Leu69Phe missense_variant 1.0
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0