TB-Profiler result

Run: ERR4831969
Summary

Run ID: ERR4831969

Sample name:

Date: 01-04-2023 21:14:38

Number of reads: 2043199

Percentage reads mapped: 98.99

Strain: lineage2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.1 East-Asian (non-Beijing) None 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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764724 p.Phe452Ser missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289204 p.Phe13Ser missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760566 p.Ser254Pro missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304443 p.Ala505Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472241 n.396A>G non_coding_transcript_exon_variant 0.13
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.18
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.18
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.11
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.16
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.11
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.11
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.11
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.12
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.12
rrl 1474717 n.1060A>G non_coding_transcript_exon_variant 0.13
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.15
rrl 1474743 n.1086T>G non_coding_transcript_exon_variant 0.18
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.16
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 0.12
rrl 1475077 n.1420C>A non_coding_transcript_exon_variant 0.13
rrl 1476034 n.2377C>A non_coding_transcript_exon_variant 0.14
inhA 1674300 c.99C>A synonymous_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156428 c.-317C>A upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169732 p.Asn294Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.27
Rv2752c 3065518 p.Leu225Pro missense_variant 1.0
thyX 3067400 c.546C>T synonymous_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246088 c.-426A>G upstream_gene_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407926 c.276dupA frameshift_variant 1.0