TB-Profiler result

Run: ERR2229561
Summary

Run ID: ERR2229561

Sample name:

Date: 31-03-2023 17:19:14

Number of reads: 1049521

Percentage reads mapped: 99.16

Strain: lineage4.8

Drug-resistance: Sensitive

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
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
mshA 576115 c.768G>A synonymous_variant 0.29
mshA 576207 p.Ala287Asp missense_variant 0.22
mshA 576745 c.1398G>C synonymous_variant 0.14
mshA 576752 p.Pro469Ala missense_variant 0.14
ccsA 620528 p.Ala213Val missense_variant 0.13
rpoB 762789 p.Leu995Met missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775871 p.Ile870Met missense_variant 0.14
mmpL5 775968 c.2512delA frameshift_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303786 p.His286Asn missense_variant 0.11
fbiC 1304973 c.2043C>A synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474605 n.948A>G non_coding_transcript_exon_variant 0.11
rrl 1476300 n.2644delA non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
rpsA 1833392 c.-150C>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154761 p.Gly451Arg missense_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.22
PPE35 2169272 c.1341C>G synonymous_variant 0.22
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2169287 c.1326T>C synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.52
PPE35 2170053 p.Thr187Ser missense_variant 0.52
PPE35 2170147 p.Ser156Ala missense_variant 0.14
PPE35 2170159 p.Ala152Ser missense_variant 0.12
PPE35 2170189 p.Glu142Gln missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289563 c.-322G>T upstream_gene_variant 0.14
kasA 2519140 c.1026G>C synonymous_variant 0.15
kasA 2519143 c.1029G>C synonymous_variant 0.14
kasA 2519153 p.Ile347Val missense_variant 0.23
kasA 2519167 c.1053T>C synonymous_variant 0.15
kasA 2519171 p.Leu353Val missense_variant 0.14
folC 2747088 p.Ala171Ser missense_variant 0.17
pepQ 2860144 p.Val92Gly missense_variant 0.21
ribD 2987098 p.Thr87Asn missense_variant 0.13
Rv2752c 3066382 c.-191G>T upstream_gene_variant 0.12
fbiD 3339347 p.Ala77Val missense_variant 0.13
Rv3083 3448427 c.-77C>A upstream_gene_variant 0.13
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612901 c.216C>T synonymous_variant 0.14
ddn 3986657 c.-186delG upstream_gene_variant 0.11
clpC1 4040259 p.Glu149Ala missense_variant 0.14
embC 4240446 p.Pro195Gln missense_variant 0.15
embC 4241230 c.1368A>G synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242887 p.Trp1009Arg missense_variant 0.14
embA 4243395 p.Ile55Phe missense_variant 0.15
embA 4243594 p.Ser121Leu missense_variant 0.12
embA 4246030 p.Pro933Gln missense_variant 0.25
embB 4246544 p.Thr11Pro missense_variant 0.4
embB 4246548 p.Pro12Gln missense_variant 0.3
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4246567 c.54_55insT frameshift_variant 0.25
embB 4249011 p.Leu833Arg missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0