TB-Profiler result

Run: ERR2229586
Summary

Run ID: ERR2229586

Sample name:

Date: 31-03-2023 17:20:24

Number of reads: 617930

Percentage reads mapped: 98.83

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
embB 4247642 p.Val377Met missense_variant 0.12 ethambutol
embB 4247850 p.Pro446His missense_variant 0.2 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 5949 p.Ala237Glu missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8689 p.Ala463Val missense_variant 0.22
gyrA 9054 p.Pro585Thr missense_variant 0.2
gyrA 9085 p.His595Arg missense_variant 0.22
gyrA 9289 p.Val663Glu missense_variant 0.13
fgd1 490837 p.Glu19* stop_gained 0.13
fgd1 491034 c.252C>A synonymous_variant 0.25
mshA 575716 c.369C>T synonymous_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.33
ccsA 620716 p.Ala276Met missense_variant 0.33
rpoB 759989 c.183G>T synonymous_variant 0.18
rpoB 761872 p.Arg689Leu missense_variant 0.2
rpoB 762427 p.Ser874Tyr missense_variant 0.18
rpoC 766325 p.Gly986Cys missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776093 c.2388C>A synonymous_variant 0.33
mmpL5 777128 c.1353A>G synonymous_variant 0.12
mmpL5 777532 p.Ile317Val missense_variant 0.12
mmpL5 778056 p.Ser142Ile missense_variant 0.29
mmpL5 778624 c.-144C>A upstream_gene_variant 0.17
mmpL5 779154 c.-674T>C upstream_gene_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781614 p.Val19Phe missense_variant 0.22
rplC 800792 c.-17G>T upstream_gene_variant 0.17
fbiC 1303055 p.Asp42Val missense_variant 0.25
fbiC 1303606 p.Lys226Glu missense_variant 0.29
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303785 c.855G>A synonymous_variant 0.4
fbiC 1303919 p.Arg330His missense_variant 0.2
Rv1258c 1406731 c.610C>A synonymous_variant 0.2
embR 1416430 c.918G>C synonymous_variant 0.12
atpE 1460946 c.-99A>G upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473237 n.1392C>A non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474185 n.528G>T non_coding_transcript_exon_variant 0.15
rrl 1474243 n.586G>T non_coding_transcript_exon_variant 0.17
rrl 1474390 n.733C>A non_coding_transcript_exon_variant 0.17
rrl 1475235 n.1582delA non_coding_transcript_exon_variant 0.29
rrl 1475257 n.1600C>A non_coding_transcript_exon_variant 0.18
rrl 1475448 n.1791T>C non_coding_transcript_exon_variant 0.29
fabG1 1673686 p.Glu83Lys missense_variant 0.18
inhA 1674194 c.-8G>C upstream_gene_variant 0.17
rpsA 1834772 p.Arg411Ser missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918530 c.591G>T synonymous_variant 0.17
ndh 2102072 p.Ala324Asp missense_variant 0.12
ndh 2102112 p.Ile311Val missense_variant 0.17
ndh 2102150 p.Asp298Val missense_variant 0.22
katG 2156453 c.-342C>A upstream_gene_variant 0.13
PPE35 2167814 c.2799C>T synonymous_variant 0.33
PPE35 2167965 p.Ala883Gly missense_variant 0.18
PPE35 2167967 c.2646A>C synonymous_variant 0.18
PPE35 2168061 p.Ile851Asn missense_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169178 p.Ala479Ser missense_variant 0.15
PPE35 2169488 c.1125G>C synonymous_variant 0.15
PPE35 2169491 c.1122T>C synonymous_variant 0.15
PPE35 2169602 c.1011C>A synonymous_variant 0.15
PPE35 2169902 p.Leu237Phe missense_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.34
PPE35 2170053 p.Thr187Ser missense_variant 0.36
Rv1979c 2222514 c.651G>T synonymous_variant 0.12
Rv1979c 2223191 c.-27G>A upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288972 c.270C>T synonymous_variant 0.2
pncA 2289168 p.Ala25Asp missense_variant 0.17
pncA 2289799 c.-558G>A upstream_gene_variant 0.25
kasA 2517958 c.-157A>T upstream_gene_variant 0.18
ahpC 2725969 c.-224C>T upstream_gene_variant 0.15
ahpC 2726540 c.348C>T synonymous_variant 0.12
folC 2746541 p.Ala353Val missense_variant 0.4
folC 2747435 p.Asp55Val missense_variant 0.15
pepQ 2859802 p.Arg206Leu missense_variant 0.2
Rv2752c 3064710 c.1482G>T synonymous_variant 0.18
Rv2752c 3065365 p.Leu276Pro missense_variant 0.29
Rv2752c 3066300 c.-109G>T upstream_gene_variant 0.25
thyX 3067547 c.399C>T synonymous_variant 0.15
thyX 3068015 c.-70T>G upstream_gene_variant 0.14
thyA 3073835 p.Val213Phe missense_variant 0.15
thyA 3073844 p.Asp210Tyr missense_variant 0.17
thyA 3074516 c.-45C>A upstream_gene_variant 0.22
thyA 3074629 c.-158C>T upstream_gene_variant 0.17
thyA 3074641 c.-170C>T upstream_gene_variant 0.22
ald 3086638 c.-182G>T upstream_gene_variant 0.14
ald 3087786 p.Glu323* stop_gained 0.18
fprA 3474694 c.688C>T synonymous_variant 0.29
Rv3236c 3612072 p.Pro349Thr missense_variant 0.15
Rv3236c 3612709 c.408G>T synonymous_variant 0.29
fbiA 3640522 c.-21C>A upstream_gene_variant 0.18
fbiB 3640857 c.-678G>T upstream_gene_variant 0.31
fbiB 3641625 p.Ala31Thr missense_variant 0.2
fbiB 3641880 p.Ser116Ala missense_variant 0.33
fbiB 3642082 p.Tyr183Phe missense_variant 0.22
alr 3840570 p.Val284Ala missense_variant 0.33
alr 3841322 c.99C>T synonymous_variant 0.2
alr 3841500 c.-80C>T upstream_gene_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.21
rpoA 3877850 p.Gly220Cys missense_variant 0.18
rpoA 3877947 c.561C>A synonymous_variant 0.29
rpoA 3877959 c.549C>T synonymous_variant 0.4
clpC1 4038573 p.Asn711Ile missense_variant 0.18
clpC1 4039003 p.Asn568Asp missense_variant 0.17
clpC1 4039169 p.Glu512Asp missense_variant 0.29
clpC1 4040085 p.Arg207Leu missense_variant 0.29
panD 4043912 c.369delT frameshift_variant 0.17
embC 4240595 p.Leu245Met missense_variant 0.25
embC 4240653 p.Pro264His missense_variant 0.17
embC 4242143 p.Pro761Ser missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243067 p.Asp1069Asn missense_variant 0.14
embA 4245250 p.His673Leu missense_variant 0.14
embA 4245509 c.2277A>T synonymous_variant 0.25
embA 4245806 c.2576delT frameshift_variant 0.33
embA 4245834 c.2603_2609delTGGTGGT frameshift_variant 0.25
embA 4245844 p.Val871Glu missense_variant 0.25
embA 4245846 p.Ser872Thr missense_variant 0.25
embA 4245848 c.2616_2617insACCACCA frameshift_variant 0.25
embA 4246501 p.Ile1090Ser missense_variant 0.29
embB 4246704 p.Leu64Pro missense_variant 0.17
embB 4246870 p.Ser119Arg missense_variant 0.14
embB 4247028 p.Leu172Arg missense_variant 0.25
embB 4248266 p.Leu585Met missense_variant 0.15
embB 4249593 p.Thr1027Met missense_variant 0.25
embB 4249726 c.3213C>A synonymous_variant 0.33
aftB 4267075 p.Leu588Phe missense_variant 0.25
aftB 4267132 p.Pro569Ala missense_variant 0.17
ubiA 4269113 p.Asp241Tyr missense_variant 0.15
ethR 4328101 p.Ala185Ser missense_variant 0.18
whiB6 4338321 c.201C>A synonymous_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408028 p.Leu59Val missense_variant 0.13
gid 4408290 c.-88G>T upstream_gene_variant 0.18
gid 4408300 c.-98T>A upstream_gene_variant 0.18
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0