TB-Profiler result

Run: ERR2124091
Summary

Run ID: ERR2124091

Sample name:

Date: 31-03-2023 15:52:05

Number of reads: 7280066

Percentage reads mapped: 99.22

Strain: lineage4.3.4.2

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.99
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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 0.98 ethambutol
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 0.98
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.21
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.24
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.33
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.37
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.44
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.53
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.53
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.55
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.31
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.28
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.14
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.46
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.45
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.43
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.4
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.37
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.37
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.37
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.17
rrs 1472697 n.852T>G non_coding_transcript_exon_variant 0.15
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.28
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.28
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.27
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.31
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.65
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.67
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.68
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.67
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.34
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.34
rrs 1472836 n.991G>C non_coding_transcript_exon_variant 0.24
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.15
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.29
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.29
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.33
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.32
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.32
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.32
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.32
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.32
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.33
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.1
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.2
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.2
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.19
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.19
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.19
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.24
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.25
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.27
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.27
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.18
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.18
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.16
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.16
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.14
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.12
Rv2752c 3065293 p.Val300Ala missense_variant 0.99
thyA 3073806 c.666C>G synonymous_variant 0.19
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.12
embC 4239763 c.-100C>T upstream_gene_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408141 p.Arg21Pro missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0