TB-Profiler result

Run: ERR3014590
Summary

Run ID: ERR3014590

Sample name:

Date: 01-04-2023 00:07:57

Number of reads: 2287229

Percentage reads mapped: 87.47

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.94 streptomycin
tlyA 1918350 c.412_413dupGG frameshift_variant 1.0 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155289 p.Thr275Ala missense_variant 1.0 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 0.48 pyrazinamide, pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 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 8602 p.Ala434Glu missense_variant 1.0
rpoB 761655 p.Ala617Thr missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778086 c.394delG frameshift_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406343 p.Asn333Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.13
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.15
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.19
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.19
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.24
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.24
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.24
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.28
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.26
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.27
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.26
rrs 1472574 n.729T>C non_coding_transcript_exon_variant 0.26
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.26
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.26
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.36
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.28
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.19
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.19
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.18
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.1
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.11
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.11
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.17
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.19
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.18
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.18
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.14
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.15
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.11
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.11
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.11
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.15
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.12
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.13
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.15
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.12
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.12
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.12
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.12
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.19
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.19
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.19
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.27
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.35
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.36
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.32
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.34
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.35
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.36
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.37
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.38
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.38
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.27
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.24
inhA 1673496 c.-706G>A upstream_gene_variant 1.0
inhA 1674990 c.789C>T synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155735 p.Met126Thr missense_variant 0.14
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518224 p.Leu37Ser missense_variant 0.11
folC 2747420 p.Pro60Leu missense_variant 1.0
folC 2747480 p.Glu40Ala missense_variant 1.0
thyA 3074156 c.315dupC frameshift_variant 0.1
thyA 3074236 p.Ile79Thr missense_variant 1.0
ald 3087251 c.434dupG frameshift_variant 0.97
alr 3840952 p.Lys157Glu missense_variant 1.0
clpC1 4038496 p.Arg737Trp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245735 p.Ala835Thr missense_variant 0.11
aftB 4268621 p.Trp72* stop_gained 0.17
ubiA 4269477 p.Met119Ile missense_variant 0.11
ethA 4326111 p.Trp455Arg missense_variant 1.0
ethA 4327326 p.Tyr50Asn missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0