TB-Profiler result

Run: ERR2229720

Summary

Run ID: ERR2229720

Sample name:

Date: 31-03-2023 17:29:36

Number of reads: 1057933

Percentage reads mapped: 99.17

Strain: lineage4.8

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
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
embC 4240592 p.Ala244Thr missense_variant 0.14 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491315 p.Gly178Asp missense_variant 0.12
fgd1 491321 p.Ala180Val missense_variant 0.13
mshA 576232 p.Ile295Met missense_variant 0.2
ccsA 620117 p.Val76Asp missense_variant 0.15
ccsA 620212 p.Gly108Arg missense_variant 0.14
rpoB 761389 p.Asp528Gly missense_variant 0.12
rpoB 762273 p.Ala823Ser missense_variant 0.12
rpoB 763041 p.Leu1079Met missense_variant 0.13
rpoC 763220 c.-150G>C upstream_gene_variant 0.14
rpoB 763222 p.Ile1139Thr missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776080 p.Ala801Ser missense_variant 0.11
mmpL5 776081 c.2400G>A synonymous_variant 0.11
mmpL5 776087 c.2394C>G synonymous_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303799 p.Val290Ala missense_variant 0.11
fbiC 1304270 p.Val447Asp missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472761 n.916A>T non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476292 n.2635G>C non_coding_transcript_exon_variant 0.25
rrl 1476467 n.2810A>G non_coding_transcript_exon_variant 0.18
rrl 1476521 n.2864C>A non_coding_transcript_exon_variant 0.29
fabG1 1673380 c.-60C>G upstream_gene_variant 0.3
fabG1 1673751 p.Lys104Asn missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103240 c.-198C>G upstream_gene_variant 0.12
katG 2154081 c.2031C>T synonymous_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.24
PPE35 2167967 c.2646A>C synonymous_variant 0.24
PPE35 2168047 p.Leu856Val missense_variant 0.12
PPE35 2168051 c.2562G>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169125 p.Val496Ile missense_variant 0.23
PPE35 2170048 p.Leu189Val missense_variant 0.59
PPE35 2170053 p.Thr187Ser missense_variant 0.61
PPE35 2170147 p.Ser156Ala missense_variant 0.14
PPE35 2170235 c.378T>C synonymous_variant 0.13
PPE35 2170238 c.375T>G synonymous_variant 0.13
PPE35 2170244 c.369G>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289525 c.-284G>T upstream_gene_variant 0.14
kasA 2519140 c.1026G>C synonymous_variant 0.15
kasA 2519143 c.1029G>C synonymous_variant 0.15
pepQ 2859900 p.Ser173Arg missense_variant 0.18
thyX 3068011 c.-66C>T upstream_gene_variant 0.15
thyX 3068015 c.-70T>G upstream_gene_variant 0.15
whiB7 3568720 c.-41C>T upstream_gene_variant 0.13
Rv3236c 3613308 c.-192T>A upstream_gene_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.18
rpoA 3877885 p.Leu208Arg missense_variant 0.13
rpoA 3877891 p.Asp206Val missense_variant 0.12
rpoA 3877897 p.Pro204Gln missense_variant 0.13
rpoA 3878545 c.-38A>G upstream_gene_variant 0.5
clpC1 4039691 c.1014G>C synonymous_variant 0.11
clpC1 4039829 p.Leu292Phe missense_variant 0.14
embC 4241781 p.Trp640Leu missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243551 p.Val107Phe missense_variant 0.17
embA 4244451 p.Pro407Thr missense_variant 0.17
embA 4246026 p.Ala932Ser missense_variant 0.12
embA 4246069 p.Pro946Gln missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.62
embB 4246555 c.42G>C synonymous_variant 0.67
embB 4246556 p.Ala15Pro missense_variant 0.67
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4246567 c.54G>T synonymous_variant 0.4
embB 4249664 p.Thr1051Ser missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408215 c.-13G>A upstream_gene_variant 0.15
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0