TB-Profiler result

Run: ERR4797717

Summary

Run ID: ERR4797717

Sample name:

Date: 16-08-2022 02:28:20

Number of reads: 2513702

Percentage reads mapped: 96.44

Strain: lineage2.2.1

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288713 p.Thr177Pro missense_variant 1.0 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
thyA 3073347 c.-874_*332del transcript_ablation 1.0 para-aminosalicylic_acid
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
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764840 p.Ile491Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.1
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.1
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.11
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.11
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.11
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.11
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.11
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.11
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.11
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.11
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.11
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.11
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.1
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.13
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.13
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.12
rrl 1474316 n.659T>C non_coding_transcript_exon_variant 0.11
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.14
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.16
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.16
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.16
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.16
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.19
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.14
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.1
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.98
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223332 c.-168A>G upstream_gene_variant 1.0
Rv2752c 3065903 p.Arg97* stop_gained 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878630 c.-123G>C upstream_gene_variant 0.1
embC 4241022 p.Ala387Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338334 p.Ala63Glu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0