TB-Profiler result

Run: ERR4817709
Summary

Run ID: ERR4817709

Sample name:

Date: 01-04-2023 15:08:51

Number of reads: 5059537

Percentage reads mapped: 97.53

Strain: lineage4.6.2.2

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
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 0.38 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 1472251 n.406G>A non_coding_transcript_exon_variant 0.12
rrs 1472440 n.595G>A non_coding_transcript_exon_variant 0.12
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.22
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.29
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.39
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.41
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.46
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.45
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.43
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.48
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.44
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.44
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.24
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.12
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.23
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.25
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.36
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.36
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.44
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.35
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.33
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.16
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 0.27
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.15
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.15
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.21
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.14
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.11
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.17
rrs 1473193 n.1348G>A non_coding_transcript_exon_variant 0.13
rrs 1473204 n.1359C>T non_coding_transcript_exon_variant 0.13
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.16
rrs 1473215 n.1370A>G non_coding_transcript_exon_variant 0.14
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.67
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.67
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.67
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 1.0
rrl 1474783 n.1126G>T non_coding_transcript_exon_variant 1.0
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.67
rrl 1474837 n.1180A>G non_coding_transcript_exon_variant 0.5
rrl 1474852 n.1195T>C non_coding_transcript_exon_variant 0.5
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.22
rrl 1475735 n.2078T>C non_coding_transcript_exon_variant 0.23
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.21
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.23
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.21
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.2
rrl 1475783 n.2126T>C non_coding_transcript_exon_variant 0.18
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.2
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.19
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.19
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.15
rrl 1475897 n.2240T>G non_coding_transcript_exon_variant 0.14
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.14
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.14
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.14
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.15
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.11
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.1
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.13
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.14
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.11
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 0.99
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