TB-Profiler result

Run: ERR2229384
Summary

Run ID: ERR2229384

Sample name:

Date: 31-03-2023 17:08:54

Number of reads: 844141

Percentage reads mapped: 98.78

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
gyrB 6202 c.963C>T synonymous_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7395 p.Ala32Ser missense_variant 0.13
gyrA 9261 p.Arg654Ser missense_variant 0.15
mshA 575949 p.Val201Gly missense_variant 0.33
mshA 576734 p.Leu463Met missense_variant 0.12
ccsA 620364 c.474C>A synonymous_variant 0.15
rpoB 761152 p.Leu449Gln missense_variant 0.22
rpoC 764206 c.837T>C synonymous_variant 0.18
rpoC 764336 p.Glu323Gln missense_variant 0.18
rpoC 764693 p.Gly442Ser missense_variant 0.18
rpoC 764899 p.Gln510His missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776192 c.2289G>T synonymous_variant 0.17
mmpL5 777128 c.1353A>G synonymous_variant 0.12
mmpL5 777884 c.597C>A synonymous_variant 0.15
mmpL5 778128 p.Ala118Asp missense_variant 0.29
rpsL 781380 c.-180C>T upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781764 p.Gly69Ser missense_variant 0.15
rpsL 781848 p.Ile97Phe missense_variant 0.2
fbiC 1303512 c.582T>C synonymous_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416805 c.543A>G synonymous_variant 0.12
embR 1417201 c.147C>A synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472805 n.960C>G non_coding_transcript_exon_variant 0.2
rrs 1472814 n.969G>T non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475339 n.1682T>C non_coding_transcript_exon_variant 0.22
rrl 1475663 n.2006G>T non_coding_transcript_exon_variant 0.12
rrl 1475905 n.2248G>A non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.21
fabG1 1673349 c.-91G>C upstream_gene_variant 0.21
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
fabG1 1674074 p.Gly212Asp missense_variant 0.4
inhA 1674300 c.99C>A synonymous_variant 0.4
rpsA 1833743 p.Leu68Met missense_variant 0.15
rpsA 1834495 p.Glu318Asp missense_variant 0.25
rpsA 1834521 p.Ala327Asp missense_variant 0.25
rpsA 1834667 p.Ala376Ser missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154075 c.2037G>A synonymous_variant 0.17
katG 2154309 c.1803C>T synonymous_variant 0.2
katG 2156482 c.-371G>A upstream_gene_variant 0.25
PPE35 2168220 p.Ala798Glu missense_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169044 c.1569G>C synonymous_variant 0.22
PPE35 2169488 c.1125G>C synonymous_variant 0.13
PPE35 2169581 c.1032C>G synonymous_variant 0.14
PPE35 2169587 c.1026G>A synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.76
PPE35 2170053 p.Thr187Ser missense_variant 0.75
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518366 c.252G>A synonymous_variant 0.18
ahpC 2726283 p.Pro31Thr missense_variant 0.13
ahpC 2726594 c.402G>A synonymous_variant 0.2
folC 2747245 c.354G>T synonymous_variant 0.29
pepQ 2859468 c.948_950delACT disruptive_inframe_deletion 0.18
pepQ 2859543 c.876C>T synonymous_variant 0.29
pepQ 2860081 p.Ala113Glu missense_variant 0.2
pepQ 2860211 p.Asp70Asn missense_variant 0.29
Rv2752c 3065801 p.Gly131Ser missense_variant 0.12
Rv2752c 3065929 p.Gly88Val missense_variant 0.33
thyX 3067340 c.606G>A synonymous_variant 0.27
ald 3087367 p.Ala183Glu missense_variant 0.18
fbiD 3339555 c.438C>A synonymous_variant 0.15
Rv3236c 3612036 p.Val361Ile missense_variant 0.12
alr 3840600 p.Ala274Val missense_variant 0.14
alr 3841009 p.Leu138Ile missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.26
rpoA 3877526 p.Gly328Ser missense_variant 0.33
rpoA 3878034 c.474A>G synonymous_variant 0.15
clpC1 4039031 c.1674T>C synonymous_variant 0.14
clpC1 4039161 p.His515Gly missense_variant 0.12
clpC1 4039169 p.Glu512Asp missense_variant 0.13
clpC1 4039645 p.His354Asp missense_variant 0.2
clpC1 4039654 p.Thr351Ser missense_variant 0.25
clpC1 4039730 c.975C>G synonymous_variant 0.13
clpC1 4040144 c.561G>C synonymous_variant 0.22
clpC1 4040487 p.Ala73Glu missense_variant 0.14
panD 4044084 p.Ser66Arg missense_variant 0.25
embC 4242025 c.2163A>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242730 c.-503C>T upstream_gene_variant 0.18
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.83
embB 4246556 p.Ala15Pro missense_variant 0.83
embB 4246563 p.Leu17Trp missense_variant 0.86
embB 4246567 c.54G>T synonymous_variant 0.38
embB 4247192 c.679_680insGT frameshift_variant 0.22
embB 4249315 p.Phe934Leu missense_variant 0.25
embB 4249320 p.Arg936Leu missense_variant 0.25
aftB 4268208 p.Arg210Leu missense_variant 0.15
aftB 4268516 c.321A>T synonymous_variant 0.29
ethA 4326082 p.Asp464Glu missense_variant 0.2
ethR 4327663 p.Asp39Tyr missense_variant 0.15
ethR 4327791 c.244delC frameshift_variant 0.25
whiB6 4338243 c.279C>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0