TB-Profiler result

Run: ERR2513742
Summary

Run ID: ERR2513742

Sample name:

Date: 13-08-2022 09:57:16

Number of reads: 1495462

Percentage reads mapped: 99.12

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 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 7582 p.Asp94Ala missense_variant 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289205 c.36_37insGCCAGCGAGCCACCCTCGCAGAAGTCG conservative_inframe_insertion 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326181 c.1292delT frameshift_variant 1.0 ethionamide
gid 4408100 c.102delG frameshift_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 9647 c.2346C>T synonymous_variant 1.0
rpoB 761568 p.Ile588Val missense_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 1472089 n.244C>T non_coding_transcript_exon_variant 1.0
rrs 1472183 n.338C>T non_coding_transcript_exon_variant 0.1
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.15
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.15
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.15
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.15
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.12
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.12
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.12
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.12
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.15
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.15
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.2
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.18
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.3
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.18
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.2
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.4
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.3
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.2
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.2
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.2
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.18
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.15
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.15
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.18
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.18
rrl 1474381 n.724T>C non_coding_transcript_exon_variant 0.14
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.14
rrl 1475754 n.2097G>A non_coding_transcript_exon_variant 0.14
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.14
rrl 1475762 n.2105G>C non_coding_transcript_exon_variant 0.14
rrl 1475774 n.2117C>T non_coding_transcript_exon_variant 0.14
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.16
PPE35 2167868 c.2745A>C synonymous_variant 0.14
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519057 p.Thr315Ser missense_variant 0.12
kasA 2519062 c.948T>G synonymous_variant 0.12
ahpC 2726341 p.Val50Gly missense_variant 0.17
thyA 3074127 c.345G>A synonymous_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
ald 3087894 c.1076dupT frameshift_variant 1.0
fprA 3474119 p.Met38Thr missense_variant 1.0
clpC1 4039003 p.Asn568Asp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248317 p.Val602Pro missense_variant 0.1
embB 4248321 p.Gly603Ala missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0