TB-Profiler result

Run: ERR2229145
Summary

Run ID: ERR2229145

Sample name:

Date: 31-03-2023 16:44:17

Number of reads: 409153

Percentage reads mapped: 98.54

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 8579 p.Asp426Glu missense_variant 0.12
gyrA 9430 p.Arg710Leu missense_variant 0.29
fgd1 490792 p.Leu4Met missense_variant 0.13
fgd1 491391 c.609C>T synonymous_variant 0.2
fgd1 491551 p.Glu257* stop_gained 0.15
mshA 576096 p.Gly250Asp missense_variant 0.33
mshA 576667 c.1320T>C synonymous_variant 0.12
ccsA 620351 p.Arg154Leu missense_variant 0.22
ccsA 620685 p.Glu265Asp missense_variant 0.2
rpoB 760972 p.Arg389Leu missense_variant 0.13
rpoB 761219 c.1413G>T synonymous_variant 0.15
rpoC 762557 c.-813G>T upstream_gene_variant 0.2
rpoB 763128 c.3323delA frameshift_variant 0.18
rpoC 766018 p.Asp883Glu missense_variant 0.25
rpoC 766506 p.Ile1046Asn missense_variant 0.25
rpoC 767265 p.Ala1299Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776207 c.2274G>T synonymous_variant 0.22
mmpL5 776317 p.His722Tyr missense_variant 0.17
mmpS5 779621 c.-716G>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303262 p.Pro111Gln missense_variant 0.25
fbiC 1303336 p.Ala136Thr missense_variant 0.15
fbiC 1303662 c.732C>A synonymous_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305121 p.Asp731Asn missense_variant 0.18
fbiC 1305139 p.Thr737Ala missense_variant 0.18
Rv1258c 1406302 c.1039C>A synonymous_variant 0.22
embR 1416190 c.1158C>A synonymous_variant 0.13
embR 1416363 p.His329Asn missense_variant 0.29
embR 1416620 p.Pro243Leu missense_variant 0.14
embR 1417500 c.-153C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472023 n.178G>T non_coding_transcript_exon_variant 0.4
inhA 1673805 c.-397G>T upstream_gene_variant 0.15
fabG1 1674154 p.Val239Ile missense_variant 0.17
inhA 1674188 c.-14A>G upstream_gene_variant 0.12
inhA 1674591 p.Met130Ile missense_variant 0.2
inhA 1674755 p.Arg185Leu missense_variant 0.2
rpsA 1834312 p.Glu257Asp missense_variant 0.17
rpsA 1834464 p.Gly308Val missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918379 p.Arg147Leu missense_variant 0.2
ndh 2102215 p.Trp276Cys missense_variant 0.4
ndh 2103230 c.-188T>C upstream_gene_variant 0.14
katG 2154764 p.Val450Phe missense_variant 0.22
katG 2154908 p.Glu402* stop_gained 0.29
katG 2156206 c.-95C>A upstream_gene_variant 0.12
katG 2156286 c.-175G>T upstream_gene_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169939 p.Gly225Ala missense_variant 0.11
PPE35 2169944 c.669G>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.27
PPE35 2170307 c.306G>A synonymous_variant 0.2
PPE35 2170594 p.Pro7Thr missense_variant 0.14
PPE35 2170675 c.-63G>T upstream_gene_variant 0.13
Rv1979c 2222627 p.Gly180Cys missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223344 c.-180A>G upstream_gene_variant 0.11
kasA 2518685 p.Asp191Asn missense_variant 0.33
eis 2714396 p.Glu313Lys missense_variant 0.25
ahpC 2726465 p.Phe91Leu missense_variant 0.13
folC 2747072 p.Gly176Val missense_variant 0.29
folC 2747447 p.Ser51Ile missense_variant 0.2
pepQ 2859367 p.Met351Lys missense_variant 0.29
pepQ 2859759 c.660C>A synonymous_variant 0.2
pepQ 2859860 p.Ala187Ser missense_variant 0.22
pepQ 2860072 p.Gly116Val missense_variant 0.2
ribD 2987004 p.Asp56Tyr missense_variant 0.25
ribD 2987264 c.426G>A synonymous_variant 0.2
Rv2752c 3065963 p.Leu77Met missense_variant 0.14
Rv2752c 3066176 p.Pro6Ala missense_variant 0.22
thyX 3067444 p.Arg168Cys missense_variant 0.25
thyX 3067462 p.Leu162Met missense_variant 0.25
thyX 3067780 c.165delC frameshift_variant 0.18
ald 3086673 c.-147G>A upstream_gene_variant 0.18
ald 3087644 c.825C>T synonymous_variant 0.2
fbiD 3338921 c.-197C>A upstream_gene_variant 0.13
fbiD 3339254 p.Thr46Lys missense_variant 0.18
fbiD 3339463 p.Asp116Tyr missense_variant 0.18
fbiD 3339702 c.585G>T synonymous_variant 0.18
fbiD 3339758 p.Arg214Leu missense_variant 0.18
fprA 3473995 c.-12A>C upstream_gene_variant 0.18
Rv3236c 3612457 p.Leu220Phe missense_variant 0.29
fbiB 3642205 p.Asp224Val missense_variant 0.18
fbiB 3642753 p.Leu407Met missense_variant 0.17
fbiB 3642773 p.Asp413Glu missense_variant 0.17
alr 3840499 p.Ala308Ser missense_variant 0.15
alr 3840692 c.729C>T synonymous_variant 0.22
alr 3840879 p.Gln181Arg missense_variant 0.22
alr 3841142 c.279C>A synonymous_variant 0.5
alr 3841296 p.Leu42Gln missense_variant 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.24
rpoA 3877732 p.Arg259Leu missense_variant 0.12
clpC1 4038861 p.Arg615Leu missense_variant 0.29
clpC1 4039592 c.1113G>T synonymous_variant 0.17
clpC1 4039729 p.Asp326Tyr missense_variant 0.18
clpC1 4040369 c.336C>A synonymous_variant 0.14
clpC1 4040440 p.Glu89* stop_gained 0.29
embC 4239909 p.Ser16Tyr missense_variant 0.25
embC 4240950 p.Val363Asp missense_variant 0.33
embC 4241047 c.1185C>A synonymous_variant 0.25
embC 4241202 p.Gly447Asp missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243199 c.-34C>T upstream_gene_variant 0.2
embA 4243535 c.305delA frameshift_variant 0.13
embA 4244210 c.978G>A synonymous_variant 0.17
embA 4244226 p.Gly332* stop_gained 0.2
embA 4244448 p.Ala406Ser missense_variant 0.33
embA 4244712 p.Ala494Ser missense_variant 0.33
embA 4246495 p.Gly1088Val missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4246563 p.Leu17Trp missense_variant 0.4
embB 4247099 p.Ala196Ser missense_variant 0.33
embB 4247285 p.Pro258Thr missense_variant 0.17
aftB 4268207 c.630C>T synonymous_variant 0.17
aftB 4268228 c.609C>A synonymous_variant 0.2
aftB 4268911 c.-75G>T upstream_gene_variant 0.25
ubiA 4269181 p.Leu218Gln missense_variant 0.5
ubiA 4269509 p.Leu109Met missense_variant 0.12
aftB 4269642 c.-806G>T upstream_gene_variant 0.12
ethR 4326853 c.-696G>A upstream_gene_variant 0.12
ethA 4327361 p.Arg38Gln missense_variant 0.2
ethA 4327458 p.Asp6Asn missense_variant 0.15
ethR 4327639 p.Ala31Ser missense_variant 0.17
ethR 4328088 p.Glu180Asp missense_variant 0.14
whiB6 4338574 c.-53G>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407631 p.Cys191Tyr missense_variant 0.2
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0