TB-Profiler result

Run: ERR4972536
Summary

Run ID: ERR4972536

Sample name:

Date: 01-04-2023 21:46:03

Number of reads: 1867859

Percentage reads mapped: 94.12

Strain: lineage4.3.2

Drug-resistance: 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
lineage4.3.2 Euro-American (LAM) LAM3 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
gyrA 7581 p.Asp94Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rplC 801268 p.Cys154Arg missense_variant 1.0 linezolid
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288930 p.Ser104Arg missense_variant 1.0 pyrazinamide
ald 3087252 c.436_437dupGC frameshift_variant 0.98 cycloserine
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
gid 4407967 p.Leu79Ser missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490757 c.-26T>A upstream_gene_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576482 p.Val379Leu missense_variant 0.11
rpoB 762218 c.2412T>C synonymous_variant 0.15
rpoC 763531 c.162G>T synonymous_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 767123 p.Val1252Met missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.12
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.19
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.11
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.19
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.18
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.18
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.12
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.12
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.1
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.11
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.14
rrs 1472892 n.1047T>C non_coding_transcript_exon_variant 0.18
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.18
rrs 1472988 n.1143T>G non_coding_transcript_exon_variant 0.11
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.1
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.11
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.11
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.11
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.11
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.12
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.11
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.12
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.22
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.12
rrs 1473084 n.1239T>C non_coding_transcript_exon_variant 0.17
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.16
rrs 1473097 n.1252G>C non_coding_transcript_exon_variant 0.16
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.16
rrs 1473100 n.1255G>C non_coding_transcript_exon_variant 0.16
rrs 1473109 n.1264T>G non_coding_transcript_exon_variant 0.14
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.14
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.15
rrs 1473122 n.1281delA non_coding_transcript_exon_variant 0.18
rrs 1473134 n.1289T>C non_coding_transcript_exon_variant 0.17
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.18
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.18
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.18
rrs 1473158 n.1313T>C non_coding_transcript_exon_variant 0.17
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.17
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.17
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.18
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.19
rrl 1473701 n.44A>G non_coding_transcript_exon_variant 0.17
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.18
rrl 1476196 n.2539C>G non_coding_transcript_exon_variant 0.18
rrl 1476197 n.2540T>C non_coding_transcript_exon_variant 0.17
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.15
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.15
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.15
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.18
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.17
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.17
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.33
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.42
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.3
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.3
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.3
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.3
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.2
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.18
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.25
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.25
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.25
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.27
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.29
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.15
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.44
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.12
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.2
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.25
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.21
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.42
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.38
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.16
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.33
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.2
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.14
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.16
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.16
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.17
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.17
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.21
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.26
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.25
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.21
rrl 1476513 n.2856G>A non_coding_transcript_exon_variant 0.14
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155545 p.Asp189Glu missense_variant 0.2
Rv1979c 2221896 c.1269G>T synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747490 p.Arg37Cys missense_variant 1.0
folC 2747526 p.Ala25Ser missense_variant 0.13
Rv2752c 3065953 p.Thr80Ile missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.98
embC 4242402 p.Arg847His missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.25
ethR 4326637 c.-912T>C upstream_gene_variant 0.1
ethA 4327378 p.Tyr32* stop_gained 1.0
ethR 4327991 p.Tyr148Phe missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0