TB-Profiler result

Run: ERR2229594
Summary

Run ID: ERR2229594

Sample name:

Date: 31-03-2023 17:20:40

Number of reads: 383397

Percentage reads mapped: 98.72

Strain: lineage4

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
lineage4 Euro-American LAM;T;S;X;H None 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
pncA 2288807 p.Asp145Glu missense_variant 0.22 pyrazinamide
pncA 2289212 p.Gln10His missense_variant 0.22 pyrazinamide
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 5409 p.Ala57Val missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7684 p.Arg128Met missense_variant 0.5
gyrA 8949 p.Lys550* stop_gained 0.4
gyrA 9006 p.Phe569Ile missense_variant 0.5
mshA 575980 p.Asp211Glu missense_variant 0.25
rpoB 763204 p.Ser1133Leu missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777164 c.1317C>T synonymous_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302755 c.-176G>A upstream_gene_variant 0.22
fbiC 1303371 c.441C>A synonymous_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304112 c.1182G>C synonymous_variant 0.33
Rv1258c 1407006 p.Leu112Pro missense_variant 0.25
embR 1416686 p.Gln221Arg missense_variant 0.18
atpE 1461102 p.Gly20Cys missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472799 n.954T>A non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474572 n.915C>A non_coding_transcript_exon_variant 0.25
rrl 1474610 n.953C>T non_coding_transcript_exon_variant 0.25
rrl 1476263 n.2606C>A non_coding_transcript_exon_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.78
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918703 p.Gly255Val missense_variant 0.15
tlyA 1918717 p.Val260Leu missense_variant 0.17
katG 2155823 p.His97Asn missense_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 0.17
PPE35 2167931 c.2682C>T synonymous_variant 0.2
PPE35 2167965 p.Ala883Gly missense_variant 0.2
PPE35 2167967 c.2646A>C synonymous_variant 0.18
PPE35 2168510 c.2103C>A synonymous_variant 0.33
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.13
PPE35 2169287 c.1326T>C synonymous_variant 0.12
PPE35 2169308 c.1305C>T synonymous_variant 0.12
PPE35 2169311 c.1302G>C synonymous_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.32
PPE35 2170136 c.477G>T synonymous_variant 0.14
PPE35 2170528 p.Ser29Ala missense_variant 0.2
Rv1979c 2222088 c.1077G>A synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.17
kasA 2519105 p.Cys331Gly missense_variant 0.33
ahpC 2726201 c.9G>A synonymous_variant 0.2
folC 2747184 p.Gln139* stop_gained 0.5
fprA 3474025 p.Ala7Thr missense_variant 0.33
whiB7 3568862 c.-183C>A upstream_gene_variant 0.22
fbiA 3640466 c.-77T>C upstream_gene_variant 0.25
fbiB 3641439 c.-96C>T upstream_gene_variant 0.25
alr 3841546 c.-126C>A upstream_gene_variant 0.15
alr 3841612 c.-193_-192insC upstream_gene_variant 0.17
rpoA 3878297 c.210delA frameshift_variant 0.18
clpC1 4039274 c.1431G>A synonymous_variant 0.4
panD 4044327 c.-46G>T upstream_gene_variant 0.18
embC 4240612 p.Ile250Met missense_variant 0.4
embC 4241421 p.Glu520Gly missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243689 p.Met153Leu missense_variant 0.18
embA 4245417 p.Gly729Arg missense_variant 0.25
embA 4245882 p.Gly884Cys missense_variant 0.22
embB 4245941 c.-573C>T upstream_gene_variant 0.4
embB 4246544 p.Thr11Pro missense_variant 0.67
embB 4247008 p.Lys165Asn missense_variant 0.17
embB 4247277 p.Pro255Leu missense_variant 0.14
embB 4248432 p.Trp640Leu missense_variant 0.12
aftB 4267527 p.Ala437Asp missense_variant 0.15
aftB 4268128 p.Pro237Thr missense_variant 0.2
ubiA 4269245 p.His197Asn missense_variant 0.25
aftB 4269264 c.-428C>A upstream_gene_variant 0.22
ubiA 4269334 p.Ala167Gly missense_variant 0.15
ubiA 4269401 p.Gln145Lys missense_variant 0.25
ethA 4326732 p.Ala248Ser missense_variant 0.13
ethA 4326896 p.Ala193Glu missense_variant 0.17
ethR 4326970 c.-579G>T upstream_gene_variant 0.33
ethA 4328338 c.-865G>C upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408195 p.Pro3Gln missense_variant 0.22
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0