TB-Profiler result

Run: ERR2515683

Summary

Run ID: ERR2515683

Sample name:

Date: 31-03-2023 21:03:46

Number of reads: 779056

Percentage reads mapped: 95.1

Strain: lineage3

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
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
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.43 streptomycin
katG 2155793 p.Trp107Arg missense_variant 0.15 isoniazid
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 8056 p.Arg252Leu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620209 c.323delG frameshift_variant 0.15
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767190 p.Pro1274His missense_variant 0.12
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 1303646 p.Ala239Glu missense_variant 0.14
embR 1417102 c.246C>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.22
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.15
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.16
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.14
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.14
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.17
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.32
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.32
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.33
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.32
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.29
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.26
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.25
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.22
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.28
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.33
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.33
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.37
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.39
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.45
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.45
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.46
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.47
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.39
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.3
rrl 1474053 n.396G>A non_coding_transcript_exon_variant 0.11
fabG1 1673518 p.Ile27Val missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101679 p.Ser455* stop_gained 0.13
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 0.93
pncA 2289478 c.-237T>A upstream_gene_variant 0.13
kasA 2518647 p.Ile178Thr missense_variant 0.1
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859710 p.Phe237Ile missense_variant 0.12
thyA 3074424 c.48G>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339324 c.207G>A synonymous_variant 0.12
Rv3083 3448897 p.Thr132Ala missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612843 c.273delG frameshift_variant 0.12
fbiB 3640629 c.-906T>C upstream_gene_variant 0.11
fbiA 3640645 p.Ser35Thr missense_variant 0.13
clpC1 4039669 p.Gln346* stop_gained 0.13
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244638 p.Val469Ala missense_variant 0.17
embB 4245824 c.-690G>A upstream_gene_variant 0.13
aftB 4268683 p.Gly52Cys missense_variant 0.15
ethA 4328212 c.-740delC upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0