TB-Profiler result

Run: ERR4815336
Summary

Run ID: ERR4815336

Sample name:

Date: 01-04-2023 13:48:24

Number of reads: 1019810

Percentage reads mapped: 89.0

Strain: lineage4.6.2.2

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
lineage4.6 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 0.97 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 6806 p.Arg523Cys missense_variant 0.17
gyrB 7155 p.Asp639Val missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8537 p.Glu412Asp missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491766 c.984G>A synonymous_variant 0.11
rpoB 759695 c.-112G>A upstream_gene_variant 0.17
rpoB 759790 c.-17T>C upstream_gene_variant 0.11
rpoB 761162 c.1356G>T synonymous_variant 0.11
rpoC 763375 c.6C>T synonymous_variant 0.11
rpoC 767073 p.Asp1235Ala missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776605 p.Arg626Ser missense_variant 0.11
mmpL5 776920 p.Arg521Gly missense_variant 0.14
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406744 c.597G>T synonymous_variant 0.13
Rv1258c 1407078 p.Gly88Ala missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.8
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 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.79
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 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.97
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.83
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.75
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.67
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.78
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.94
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.95
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.97
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.97
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 1.0
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 1.0
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 1.0
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 1.0
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 1.0
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 1.0
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 1.0
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 1.0
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 1.0
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 1.0
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.83
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.83
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.83
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.33
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.33
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.67
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.67
rpsA 1833784 c.243C>T synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918528 p.Val197Leu missense_variant 0.14
ndh 2102638 c.405A>T synonymous_variant 0.12
PPE35 2168742 p.Gly624Asp missense_variant 0.14
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223073 p.Gly31Asp missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746648 c.951G>C synonymous_variant 0.15
thyX 3067474 p.Pro158Ala missense_variant 1.0
thyA 3074256 c.216G>C synonymous_variant 0.12
thyA 3074476 c.-5C>G upstream_gene_variant 0.12
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475300 p.Ala432Ser missense_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
embC 4241683 c.1821G>T synonymous_variant 0.29
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244046 p.Ser272Pro missense_variant 0.1
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