TB-Profiler result

Run: ERR2229380
Summary

Run ID: ERR2229380

Sample name:

Date: 31-03-2023 17:08:51

Number of reads: 1036891

Percentage reads mapped: 98.94

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7837 p.Gly179Val missense_variant 0.18
fgd1 491373 c.591C>A synonymous_variant 0.29
fgd1 491540 p.Ser253* stop_gained 0.12
mshA 576108 p.Ala254Gly missense_variant 0.33
ccsA 620202 c.312G>A synonymous_variant 0.22
rpoB 760835 c.1029C>T synonymous_variant 0.12
rpoC 763710 p.Leu114Pro missense_variant 0.12
rpoC 765932 p.Gly855Cys missense_variant 0.33
rpoC 766390 c.3021C>A synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776318 c.2163C>T synonymous_variant 0.14
mmpL5 776723 p.Tyr586* stop_gained 0.27
mmpL5 777119 p.His454Gln missense_variant 0.15
mmpL5 777122 c.1359C>T synonymous_variant 0.15
mmpL5 777128 c.1353A>G synonymous_variant 0.15
mmpS5 778503 p.Thr135Ser missense_variant 0.13
mmpL5 778579 c.-99C>G upstream_gene_variant 0.25
mmpR5 779008 p.Val7Phe missense_variant 0.17
mmpS5 779576 c.-671C>A upstream_gene_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781453 c.-107C>T upstream_gene_variant 0.15
rpsL 781843 p.Tyr95Phe missense_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305070 p.Asp714Tyr missense_variant 0.14
embR 1416199 c.1149G>A synonymous_variant 0.17
embR 1416577 p.Gln257His missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472761 n.916A>G non_coding_transcript_exon_variant 0.11
rrl 1473640 n.-18C>G upstream_gene_variant 0.2
rrl 1474484 n.827C>G non_coding_transcript_exon_variant 0.13
rrl 1475288 n.1631G>A non_coding_transcript_exon_variant 0.17
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.41
fabG1 1673611 p.Val58Ile missense_variant 0.22
inhA 1674383 p.Leu61Pro missense_variant 0.12
inhA 1674935 p.Leu245Pro missense_variant 0.17
inhA 1674938 p.Leu246Pro missense_variant 0.18
rpsA 1834540 c.999G>A synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103006 p.Arg13Cys missense_variant 0.12
ndh 2103231 c.-189G>T upstream_gene_variant 0.17
katG 2154514 p.Pro533Gln missense_variant 0.18
katG 2154862 p.His417Arg missense_variant 0.2
katG 2155693 p.Ser140Ile missense_variant 0.25
PPE35 2167745 p.Thr956Arg missense_variant 0.4
PPE35 2167814 c.2799C>T synonymous_variant 0.38
PPE35 2167965 p.Ala883Gly missense_variant 0.21
PPE35 2167967 c.2646A>C synonymous_variant 0.21
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168894 c.1719C>G synonymous_variant 0.16
PPE35 2169278 c.1335T>C synonymous_variant 0.13
PPE35 2169281 c.1332T>G synonymous_variant 0.13
PPE35 2169287 c.1326T>C synonymous_variant 0.25
PPE35 2169293 c.1320T>C synonymous_variant 0.19
PPE35 2169717 p.Asn299Ile missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.58
PPE35 2170053 p.Thr187Ser missense_variant 0.59
PPE35 2170159 p.Ala152Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518713 p.Gly200Glu missense_variant 0.2
kasA 2519140 c.1026G>C synonymous_variant 0.17
kasA 2519143 c.1029G>C synonymous_variant 0.16
folC 2746205 p.Gly465Ala missense_variant 0.2
folC 2746750 c.849C>A synonymous_variant 0.12
folC 2747236 c.363G>C synonymous_variant 0.33
folC 2747773 c.-175G>T upstream_gene_variant 0.17
pepQ 2860602 c.-184A>C upstream_gene_variant 0.33
Rv2752c 3064608 c.1584G>T synonymous_variant 0.12
thyX 3068015 c.-70T>G upstream_gene_variant 0.16
fprA 3474144 p.Trp46Cys missense_variant 0.15
fprA 3474321 c.315C>A synonymous_variant 0.19
Rv3236c 3612472 c.645C>A synonymous_variant 0.18
fbiA 3641403 p.Cys287* stop_gained 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.22
rpoA 3877885 p.Leu208Arg missense_variant 0.13
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
ddn 3986750 c.-94A>G upstream_gene_variant 0.1
clpC1 4038293 c.2412G>A synonymous_variant 0.13
clpC1 4038877 p.Leu610Ile missense_variant 0.14
clpC1 4038997 c.1708T>C synonymous_variant 0.18
clpC1 4039003 p.Asn568Asp missense_variant 0.33
clpC1 4039031 c.1674T>C synonymous_variant 0.18
clpC1 4039526 c.1179G>C synonymous_variant 0.18
clpC1 4039870 p.Arg279Ser missense_variant 0.15
clpC1 4040144 c.561G>C synonymous_variant 0.2
panD 4044108 c.174C>T synonymous_variant 0.25
embC 4239950 c.88C>A synonymous_variant 0.15
embC 4239955 p.Tyr31* stop_gained 0.15
embC 4240132 c.270_271insT frameshift_variant 0.18
embC 4240158 p.Asn99Ser missense_variant 0.15
embC 4240186 c.324G>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243847 c.615C>A synonymous_variant 0.12
embA 4244184 p.Ser318Leu missense_variant 0.17
embA 4244196 p.Val322Phe missense_variant 0.12
embA 4244563 p.Arg444Gln missense_variant 0.18
embA 4244940 p.Trp570Arg missense_variant 0.14
embB 4246262 c.-252C>T upstream_gene_variant 0.13
embB 4246536 p.Arg8His missense_variant 0.2
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.55
embB 4246555 c.42G>C synonymous_variant 0.6
embB 4246556 p.Ala15Pro missense_variant 0.6
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.4
embB 4246714 c.201G>T synonymous_variant 0.2
embB 4247277 p.Pro255Gln missense_variant 0.22
embB 4248884 p.Asn791Asp missense_variant 0.14
embB 4248963 p.Ala817Glu missense_variant 0.14
embB 4249010 p.Leu833Met missense_variant 0.15
embB 4249350 p.Val946Ala missense_variant 0.17
aftB 4269516 c.-680G>T upstream_gene_variant 0.12
ethR 4326961 c.-588G>C upstream_gene_variant 0.15
ethR 4326964 c.-585G>A upstream_gene_variant 0.15
ethR 4326970 c.-579G>T upstream_gene_variant 0.15
ethR 4327210 c.-339G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0