TB-Profiler result

Run: ERR2229462
Summary

Run ID: ERR2229462

Sample name:

Date: 31-03-2023 17:12:59

Number of reads: 611997

Percentage reads mapped: 99.31

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
gyrA 7570 p.Ala90Val missense_variant 0.14 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
embB 4247495 p.Asp328Tyr missense_variant 0.15 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
gyrB 7188 p.Ile650Asn missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8727 p.Arg476Ser missense_variant 0.2
gyrA 9782 c.2481C>T synonymous_variant 0.12
ccsA 619905 c.15C>T synonymous_variant 0.13
rpoB 759869 c.63C>A synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775697 c.2784G>C synonymous_variant 0.12
mmpL5 775700 c.2781G>A synonymous_variant 0.12
mmpL5 775703 c.2778A>G synonymous_variant 0.12
mmpL5 775955 p.Ile842Val missense_variant 0.33
mmpL5 775966 p.Ala839Ser missense_variant 0.33
mmpL5 777119 p.His454Gln missense_variant 0.22
mmpL5 777122 c.1359C>T synonymous_variant 0.22
mmpL5 777128 c.1353A>G synonymous_variant 0.22
mmpS5 778828 p.Gln26His missense_variant 0.12
mmpR5 779362 p.Leu125Met missense_variant 0.14
mmpS5 779588 c.-683C>A upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800970 c.162T>C synonymous_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304505 c.1575G>A synonymous_variant 0.22
fbiC 1305049 p.Thr707Ser missense_variant 0.22
Rv1258c 1406259 p.Pro361Leu missense_variant 0.22
embR 1416843 p.Asp169His missense_variant 0.18
embR 1416888 p.Arg154Ser missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475761 n.2104C>A non_coding_transcript_exon_variant 0.29
rrl 1476054 n.2397T>A non_coding_transcript_exon_variant 0.17
fabG1 1673346 c.-94C>G upstream_gene_variant 0.13
fabG1 1673349 c.-91G>C upstream_gene_variant 0.12
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.56
fabG1 1673906 p.Ser156Tyr missense_variant 0.18
inhA 1674226 p.Arg9Trp missense_variant 0.14
inhA 1674339 c.138G>A synonymous_variant 0.22
rpsA 1834498 c.957C>A synonymous_variant 0.15
tlyA 1917945 c.6A>G synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102187 p.Gly286Cys missense_variant 0.17
katG 2155984 p.Leu43Arg missense_variant 0.33
PPE35 2167865 c.2748G>C synonymous_variant 0.13
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169272 c.1341C>G synonymous_variant 0.11
PPE35 2169602 c.1011C>A synonymous_variant 0.21
PPE35 2169902 p.Leu237Phe missense_variant 0.27
PPE35 2169910 p.Asn235Tyr missense_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.21
PPE35 2170053 p.Thr187Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518854 p.Leu247Pro missense_variant 0.11
kasA 2519140 c.1026G>C synonymous_variant 0.29
kasA 2519143 c.1029G>C synonymous_variant 0.29
kasA 2519153 p.Ile347Val missense_variant 0.33
eis 2714591 p.Ala248Ser missense_variant 0.11
eis 2715053 p.Arg94Ser missense_variant 0.29
Rv2752c 3065420 p.Arg258* stop_gained 0.4
Rv2752c 3065592 c.600G>T synonymous_variant 0.25
thyX 3067522 p.Thr142Ser missense_variant 0.18
ald 3086637 c.-183G>T upstream_gene_variant 0.14
ald 3086726 c.-94C>A upstream_gene_variant 0.12
ald 3087828 p.Pro337Thr missense_variant 0.15
fbiD 3339589 p.Leu158Val missense_variant 0.12
fprA 3474054 p.Phe16Leu missense_variant 0.23
Rv3236c 3613003 c.114G>A synonymous_variant 0.33
Rv3236c 3613239 c.-123A>T upstream_gene_variant 0.12
fbiB 3641467 c.-68C>T upstream_gene_variant 0.2
fbiB 3642159 p.Leu209Met missense_variant 0.14
rpoA 3877727 p.Tyr261Asn missense_variant 0.22
clpC1 4039361 c.1344C>A synonymous_variant 0.13
clpC1 4039538 c.1167C>T synonymous_variant 0.22
clpC1 4039594 p.Arg371Gly missense_variant 0.13
clpC1 4039602 p.Ala368Val missense_variant 0.14
clpC1 4039691 c.1014G>C synonymous_variant 0.18
clpC1 4039703 p.Lys334Asn missense_variant 0.27
clpC1 4039714 p.Tyr331His missense_variant 0.14
clpC1 4039730 c.975C>G synonymous_variant 0.15
clpC1 4040057 c.648C>T synonymous_variant 0.29
clpC1 4040191 p.Asp172Asn missense_variant 0.29
panD 4044236 p.Thr16Ser missense_variant 0.12
embC 4239903 c.43_45delCCA conservative_inframe_deletion 0.12
embC 4241335 p.Gln491His missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243523 c.291C>A synonymous_variant 0.17
embA 4244252 p.Ser340Arg missense_variant 0.14
embB 4246544 p.Thr11Pro missense_variant 0.13
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4247108 p.Gly199Trp missense_variant 0.13
aftB 4267970 c.867C>T synonymous_variant 0.25
aftB 4268825 c.12C>T synonymous_variant 0.15
aftB 4268866 c.-30G>T upstream_gene_variant 0.2
aftB 4269318 c.-482G>T upstream_gene_variant 0.11
ubiA 4269599 p.Glu79* stop_gained 0.14
ethA 4326155 p.Leu440Gln missense_variant 0.12
ethA 4326938 p.Val179Ala missense_variant 0.14
ethR 4328135 p.Glu196Gly missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0