TB-Profiler result

Run: ERR1035317
Summary

Run ID: ERR1035317

Sample name:

Date: 31-03-2023 10:10:53

Number of reads: 4693049

Percentage reads mapped: 97.66

Strain: lineage4.3.4.2

Drug-resistance: RR-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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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 0.98 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.77 streptomycin
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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
gyrB 6140 p.Val301Leu missense_variant 0.98
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7581 p.Asp94Arg missense_variant 0.55
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val 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 1472035 n.190G>T non_coding_transcript_exon_variant 0.11
rrs 1472042 n.197T>C non_coding_transcript_exon_variant 0.12
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.14
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.21
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.17
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.15
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.2
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.21
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.24
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.3
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.24
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.24
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.29
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.15
rrl 1473924 n.267_268insT non_coding_transcript_exon_variant 0.16
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.16
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.16
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.21
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.16
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.16
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.17
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.2
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.25
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.25
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.21
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.22
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.31
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.18
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.1
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.2
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.23
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.21
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.24
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.23
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.27
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.35
rrl 1475006 n.1349A>G non_coding_transcript_exon_variant 0.12
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.13
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.1
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.13
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.15
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.15
rrl 1475289 n.1632G>A non_coding_transcript_exon_variant 0.17
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.17
rrl 1475297 n.1640C>T non_coding_transcript_exon_variant 0.21
rrl 1475315 n.1658A>C non_coding_transcript_exon_variant 0.24
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.22
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.26
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.2
rpsA 1833726 p.Val62Glu missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156109 c.3G>T synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.96
thyA 3073806 c.666C>G synonymous_variant 0.25
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.98