TB-Profiler result

Run: ERR4815908
Summary

Run ID: ERR4815908

Sample name:

Date: 01-04-2023 14:08:18

Number of reads: 4602982

Percentage reads mapped: 99.21

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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Asp missense_variant 0.99 ethambutol
gid 4408087 c.115delC frameshift_variant 1.0 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 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
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766582 c.3213C>A synonymous_variant 0.99
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.14
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.25
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.26
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.29
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.41
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.38
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.4
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.22
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.24
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.13
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.2
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.18
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.17
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.22
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.22
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.16
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.31
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.14
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.14
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.12
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.25
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.25
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.25
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.13
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.19
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.27
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.22
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.26
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.29
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.28
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.27
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.27
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.27
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.21
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.15
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.15
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.13
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.13
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.14
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.14
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.2
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.18
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.21
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.21
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.23
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.21
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.3
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.35
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.29
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223035 p.Gly44Arg 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
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613157 c.-41G>C 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