TB-Profiler result

Run: SRR1165306
Summary

Run ID: SRR1165306

Sample name:

Date: 03-04-2023 00:01:49

Number of reads: 4477724

Percentage reads mapped: 88.12

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.98
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.Asp94Tyr missense_variant 0.13 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 0.89 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.6 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288782 p.Arg154Gly missense_variant 1.0 pyrazinamide
ald 3087278 c.464delG frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.97 ethambutol
ethA 4326279 c.1192_1194dupGTG conservative_inframe_insertion 0.95 ethionamide
ethA 4326604 c.869dupA frameshift_variant 1.0 ethionamide, ethionamide
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
rpoB 762285 p.Arg827Cys missense_variant 0.94
rpoC 762959 c.-411G>C upstream_gene_variant 0.12
rpoC 762962 c.-408C>T upstream_gene_variant 0.12
rpoC 763004 c.-366G>A upstream_gene_variant 0.12
rpoC 763007 c.-363C>T upstream_gene_variant 0.12
rpoC 764536 c.1167G>T synonymous_variant 0.11
rpoC 764575 c.1206T>G synonymous_variant 0.11
rpoC 764758 c.1389C>G synonymous_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.11
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.15
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.15
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.15
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.18
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.11
rrs 1472859 n.1014G>T non_coding_transcript_exon_variant 0.11
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.12
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.14
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.14
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.14
rrl 1473746 n.89T>C non_coding_transcript_exon_variant 0.11
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.12
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.14
rrl 1473823 n.166T>C non_coding_transcript_exon_variant 0.12
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.12
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.13
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.12
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.15
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.12
rrl 1475775 n.2118G>A non_coding_transcript_exon_variant 0.12
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.13
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.13
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.14
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.13
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.16
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.16
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.16
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.14
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.12
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.15
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.14
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.14
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.14
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.15
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.15
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067388 c.558C>G synonymous_variant 0.11
thyX 3067406 c.540A>G synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474224 c.222_223dupCC frameshift_variant 0.13
rpoA 3878619 c.-113_-112insCC upstream_gene_variant 0.11
clpC1 4039169 p.Glu512Asp missense_variant 0.1
clpC1 4039178 c.1527G>C synonymous_variant 0.11
clpC1 4039208 c.1497C>G synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4247491 c.978G>C synonymous_variant 0.11
embB 4247500 c.987C>G synonymous_variant 0.11
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0