TB-Profiler result

Run: SRR1167271
Summary

Run ID: SRR1167271

Sample name:

Date: 03-04-2023 01:59:39

Number of reads: 4534086

Percentage reads mapped: 88.1

Strain: lineage4.1.1.3

Drug-resistance: MDR-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 0.99
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
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 0.9 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.66 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.99 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 0.96 ethambutol
ethA 4326279 c.1192_1194dupGTG conservative_inframe_insertion 0.96 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
gyrB 5184 c.-56_-55insCC upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760415 c.609C>T synonymous_variant 0.12
rpoB 761570 c.1764T>C synonymous_variant 0.12
rpoB 761573 c.1767C>G synonymous_variant 0.15
rpoB 761579 c.1773G>C synonymous_variant 0.17
rpoB 761606 c.1800C>G synonymous_variant 0.19
rpoB 761612 c.1806G>T synonymous_variant 0.18
rpoB 761615 c.1809A>C synonymous_variant 0.18
rpoB 761636 c.1830G>T synonymous_variant 0.18
rpoB 761645 c.1839C>G synonymous_variant 0.18
rpoB 761648 c.1842T>C synonymous_variant 0.15
rpoB 762285 p.Arg827Cys missense_variant 0.95
rpoC 762917 c.-453C>T upstream_gene_variant 0.13
rpoC 762926 c.-444C>T upstream_gene_variant 0.11
rpoC 762929 c.-441G>C upstream_gene_variant 0.12
rpoC 762959 c.-411G>C upstream_gene_variant 0.11
rpoC 763570 c.201G>T synonymous_variant 0.13
rpoC 763573 c.204G>C synonymous_variant 0.13
rpoC 763594 c.225C>T synonymous_variant 0.12
rpoC 763933 c.564C>T synonymous_variant 0.14
rpoC 763940 p.Ala191Ser missense_variant 0.16
rpoC 763945 c.576T>C synonymous_variant 0.17
rpoC 763947 p.Ala193Val missense_variant 0.17
rpoC 763951 c.582G>C synonymous_variant 0.17
rpoC 763960 c.591T>G synonymous_variant 0.18
rpoC 763978 c.609C>T synonymous_variant 0.21
rpoC 763987 c.618C>T synonymous_variant 0.17
rpoC 763991 p.Ile208Leu missense_variant 0.16
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 1472446 n.601T>A non_coding_transcript_exon_variant 0.14
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.15
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.14
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 0.11
rrl 1473717 n.60G>T non_coding_transcript_exon_variant 0.1
rrl 1473746 n.89T>C non_coding_transcript_exon_variant 0.1
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.13
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.13
rrl 1473811 n.154C>T non_coding_transcript_exon_variant 0.11
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.12
rrl 1473823 n.166T>C non_coding_transcript_exon_variant 0.14
rrl 1473833 n.176G>A non_coding_transcript_exon_variant 0.13
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.12
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.11
rrl 1475775 n.2118G>A non_coding_transcript_exon_variant 0.14
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.11
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.11
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.11
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.14
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 0.97
katG 2155680 c.432G>C synonymous_variant 0.11
katG 2155691 c.421T>C synonymous_variant 0.16
katG 2155696 p.Ala139Val missense_variant 0.16
katG 2155716 c.394_396delCTTinsTTG synonymous_variant 0.2
katG 2155722 c.390G>C synonymous_variant 0.21
katG 2155737 c.375C>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067388 c.558C>G synonymous_variant 0.11
thyX 3067391 c.555G>C synonymous_variant 0.12
thyX 3067430 c.516C>G synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878641 c.-135delG upstream_gene_variant 0.16
clpC1 4040457 c.246_247dupCC frameshift_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267782 c.1053_1054dupGG frameshift_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0