TB-Profiler result

Run: ERR4819058
Summary

Run ID: ERR4819058

Sample name:

Date: 01-04-2023 15:54:05

Number of reads: 929460

Percentage reads mapped: 99.24

Strain: lineage3

Drug-resistance: HR-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
lineage3 East-African-Indian CAS RD750 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.33 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, 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
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761880 c.2076delC frameshift_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.97
rpoC 766582 c.3213C>A synonymous_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 1303243 p.Cys105Arg missense_variant 0.1
fbiC 1305497 p.Ala856Asp missense_variant 0.1
embR 1416196 c.1152G>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.15
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.14
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.29
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.29
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.17
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.12
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.11
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.13
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.18
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.18
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.18
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.33
rrl 1474706 n.1049G>A non_coding_transcript_exon_variant 0.4
rrl 1474717 n.1060A>T non_coding_transcript_exon_variant 0.5
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 0.33
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.11
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154568 p.Arg515His missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518456 c.342C>G synonymous_variant 0.13
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746541 p.Ala353Val missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407883 c.-76_319del frameshift_variant&start_lost 1.0