TB-Profiler result

Run: ERR4819524
Summary

Run ID: ERR4819524

Sample name:

Date: 01-04-2023 16:09:30

Number of reads: 471316

Percentage reads mapped: 95.01

Strain: lineage3

Drug-resistance: Other

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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 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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.25 streptomycin
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 6949 c.-353A>G upstream_gene_variant 0.11
gyrA 6952 c.-350C>G upstream_gene_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 1.0
gyrA 9777 p.Asn826Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762636 p.Lys944Glu missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.93
rpoB 763104 p.Ile1100Phe missense_variant 0.11
rpoC 764181 p.Asp271Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777122 c.1359C>T synonymous_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471771 n.-74delG upstream_gene_variant 1.0
rrs 1471923 n.78T>C non_coding_transcript_exon_variant 0.13
rrs 1471925 n.80_81insGCAGCTTG non_coding_transcript_exon_variant 0.13
rrs 1471928 n.83T>G non_coding_transcript_exon_variant 0.13
rrs 1471930 n.88_89delGA non_coding_transcript_exon_variant 0.13
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.13
rrs 1471978 n.133C>T non_coding_transcript_exon_variant 0.18
rrs 1471996 n.151C>T non_coding_transcript_exon_variant 0.14
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.13
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.14
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.14
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.14
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.22
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.25
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.43
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.4
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.4
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.29
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.29
rrs 1472761 n.916A>G non_coding_transcript_exon_variant 0.2
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.18
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.27
rrs 1473285 n.1442_1443delCC non_coding_transcript_exon_variant 0.27
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.23
rrs 1473293 n.1448G>T non_coding_transcript_exon_variant 0.23
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.5
rrl 1474798 n.1141C>G non_coding_transcript_exon_variant 0.5
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.6
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.75
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.75
rrl 1474825 n.1168G>A non_coding_transcript_exon_variant 0.75
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.75
rrl 1474837 n.1180A>G non_coding_transcript_exon_variant 0.75
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.75
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.6
rrl 1474901 n.1244A>G non_coding_transcript_exon_variant 0.6
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.6
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.6
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 0.5
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154495 c.1617C>A synonymous_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170769 c.-157C>T upstream_gene_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
eis 2714756 p.Pro193Ser missense_variant 1.0
eis 2715432 c.-100C>T upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3067155 c.-964C>A upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249329 p.Met939Arg missense_variant 0.17
aftB 4268197 p.Val214Met missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0