TB-Profiler result

Run: ERR2229557
Summary

Run ID: ERR2229557

Sample name:

Date: 31-03-2023 17:18:36

Number of reads: 1019268

Percentage reads mapped: 99.35

Strain: lineage4.8

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
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
katG 2155627 c.484dupG frameshift_variant 0.12 isoniazid
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 7184 p.Ser649Ala missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491594 p.Ala271Asp missense_variant 0.12
mshA 575586 p.Ala80Val missense_variant 0.15
mshA 576106 c.759C>A synonymous_variant 0.17
ccsA 620096 p.His69Leu missense_variant 0.22
ccsA 620549 p.Pro220Leu missense_variant 0.12
rpoB 762853 p.Pro1016Gln missense_variant 0.15
rpoC 764200 c.831G>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775803 p.Met893Lys missense_variant 0.13
mmpL5 776009 c.2472A>G synonymous_variant 0.2
mmpL5 776018 c.2463G>C synonymous_variant 0.18
mmpL5 776021 c.2460G>C synonymous_variant 0.18
mmpL5 777534 p.Thr316Asn missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781645 p.Gln29Arg missense_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.2
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.17
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.18
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.18
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.18
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.18
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.14
rrs 1473005 n.1160C>A non_coding_transcript_exon_variant 0.12
rrs 1473310 n.1465T>C non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475445 n.1788T>A non_coding_transcript_exon_variant 0.4
rrl 1475490 n.1833C>A non_coding_transcript_exon_variant 0.18
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.11
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.12
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.12
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.13
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.14
rrl 1475767 n.2110G>T non_coding_transcript_exon_variant 0.11
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.11
rrl 1476593 n.2936T>C non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.32
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918372 p.Gly145Ser missense_variant 0.22
ndh 2102169 p.Gln292Lys missense_variant 0.29
ndh 2102959 p.Asn28Lys missense_variant 0.15
ndh 2103190 c.-148T>G upstream_gene_variant 0.15
PPE35 2167847 c.2766A>C synonymous_variant 0.14
PPE35 2167865 c.2748G>C synonymous_variant 0.12
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2167878 p.Ser912Asn missense_variant 0.12
PPE35 2167882 p.Asn911Asp missense_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169281 c.1332T>G synonymous_variant 0.15
PPE35 2169287 c.1326T>C synonymous_variant 0.13
PPE35 2169602 c.1011C>A synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.38
PPE35 2170147 p.Ser156Ala missense_variant 0.17
PPE35 2170159 p.Ala152Ser missense_variant 0.12
PPE35 2170456 p.Val53Phe missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518068 c.-47C>A upstream_gene_variant 0.2
kasA 2518606 c.492G>C synonymous_variant 0.22
eis 2714947 p.Phe129Tyr missense_variant 0.14
folC 2746508 p.Gln364Arg missense_variant 0.12
folC 2746740 p.Ser287Pro missense_variant 0.13
ribD 2987063 c.225T>C synonymous_variant 0.4
ald 3087170 p.Tyr117* stop_gained 0.12
ald 3087512 c.693T>C synonymous_variant 0.11
Rv3236c 3613161 c.-45A>G upstream_gene_variant 0.11
fbiA 3641179 p.Pro213Thr missense_variant 0.12
fbiB 3641902 p.Val123Ala missense_variant 0.15
alr 3840212 c.1209C>T synonymous_variant 0.11
alr 3840252 p.Val390Ala missense_variant 0.11
alr 3840545 c.876C>T synonymous_variant 0.12
rpoA 3878624 c.-117C>A upstream_gene_variant 0.67
clpC1 4039866 p.Gly280Asp missense_variant 0.12
clpC1 4039942 p.Leu255Met missense_variant 0.14
embC 4241167 c.1306_1308delCTG conservative_inframe_deletion 0.12
embC 4242440 p.Val860Leu missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244847 p.Gly539Ser missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.25
embB 4246556 p.Ala15Pro missense_variant 0.25
embB 4246584 p.Arg24Pro missense_variant 0.4
embB 4248359 p.Pro616Thr missense_variant 0.12
embB 4249378 c.2865G>A synonymous_variant 0.15
aftB 4267841 c.996C>T synonymous_variant 0.11
ethA 4326089 p.Leu462Pro missense_variant 0.2
ethR 4328041 p.Thr165Pro missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0