TB-Profiler result

Run: ERR2245282
Summary

Run ID: ERR2245282

Sample name:

Date: 31-03-2023 17:37:11

Number of reads: 1710709

Percentage reads mapped: 98.94

Strain: lineage4;lineage3.1

Drug-resistance: HR-TB

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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
lineage3 East-African-Indian CAS RD750 1.0
lineage4 Euro-American LAM;T;S;X;H None 0.86
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 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
katG 2154285 p.Met609Ile missense_variant 0.25 isoniazid
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 5123 c.-117A>T upstream_gene_variant 0.29
gyrA 6946 c.-356C>T upstream_gene_variant 0.29
gyrA 7012 c.-290G>A upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7615 p.Leu105Pro missense_variant 0.67
gyrA 7985 p.Phe228Leu missense_variant 0.33
gyrA 8166 p.Glu289* stop_gained 0.17
gyrA 8189 c.888G>T synonymous_variant 0.15
gyrA 9204 p.Ser635Pro missense_variant 0.29
gyrA 9251 c.1950G>A synonymous_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9313 p.Leu671Gln missense_variant 0.33
gyrA 9695 c.2394C>A synonymous_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491792 c.1010G>A splice_region_variant&stop_retained_variant 0.2
mshA 576084 p.Val246Ala missense_variant 0.29
mshA 576108 p.Ala254Gly missense_variant 0.71
mshA 576111 p.Ala255Gly missense_variant 0.4
mshA 576284 p.Val313Phe missense_variant 0.5
ccsA 620174 p.Val95Gly missense_variant 0.5
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760189 p.Phe128Tyr missense_variant 0.4
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763714 c.345G>T synonymous_variant 0.4
rpoC 764695 c.1326T>G synonymous_variant 0.4
rpoC 764722 c.1353G>A synonymous_variant 0.25
rpoC 766548 p.Arg1060Gln missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777362 p.Met373Ile missense_variant 0.5
mmpR5 778451 c.-539C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801114 c.306C>A synonymous_variant 0.5
rplC 801417 c.609T>C synonymous_variant 0.29
fbiC 1303182 c.252C>A synonymous_variant 0.33
Rv1258c 1406794 p.Leu183Met missense_variant 0.33
embR 1416387 p.Asp321His missense_variant 0.25
embR 1416981 p.Val123Leu missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673251 c.-189T>G upstream_gene_variant 0.5
fabG1 1673276 c.-164G>T upstream_gene_variant 0.5
inhA 1674069 c.-133G>T upstream_gene_variant 0.4
rpsA 1833661 c.120A>G synonymous_variant 0.4
rpsA 1833667 c.126C>G synonymous_variant 0.4
rpsA 1833721 c.180A>G synonymous_variant 1.0
rpsA 1833724 c.183C>G synonymous_variant 1.0
rpsA 1833727 c.186G>C synonymous_variant 1.0
rpsA 1833742 c.201A>G synonymous_variant 1.0
rpsA 1833745 c.204G>C synonymous_variant 1.0
rpsA 1833748 c.207C>G synonymous_variant 1.0
rpsA 1834229 p.Gly230Cys missense_variant 0.25
ndh 2102439 c.604C>A synonymous_variant 0.29
ndh 2102897 p.His49Pro missense_variant 0.25
katG 2154068 p.Asp682Tyr missense_variant 0.4
katG 2154249 c.1863C>T synonymous_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170461 p.Gly51Glu missense_variant 1.0
PPE35 2170808 c.-196G>T upstream_gene_variant 0.18
Rv1979c 2221794 c.1371C>T synonymous_variant 0.29
Rv1979c 2222988 c.177T>C synonymous_variant 0.33
Rv1979c 2223211 c.-47G>T upstream_gene_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518802 p.Phe230Val missense_variant 0.29
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2860540 c.-122T>A upstream_gene_variant 0.5
ribD 2986858 p.Leu7His missense_variant 0.22
ribD 2986924 p.Pro29His missense_variant 0.22
ribD 2987180 c.342T>A synonymous_variant 0.5
Rv2752c 3064825 p.Asp456Ala missense_variant 0.14
Rv2752c 3064833 p.Ile453Asp missense_variant 0.14
thyX 3067510 c.436C>T synonymous_variant 1.0
thyX 3067515 p.Ser144Thr missense_variant 1.0
thyX 3067517 p.Tyr143* stop_gained 1.0
thyX 3067530 p.Ala139Ser missense_variant 1.0
thyX 3067545 p.Glu134Ala missense_variant 1.0
thyX 3067549 p.Thr133Ala missense_variant 1.0
thyX 3067556 p.His130Gln missense_variant 1.0
thyX 3067559 c.387C>G synonymous_variant 1.0
thyX 3067565 p.Asp127Glu missense_variant 1.0
thyX 3067570 p.Ala126Pro missense_variant 1.0
thyX 3067577 c.369G>A synonymous_variant 1.0
thyX 3067601 p.Arg115His missense_variant 1.0
thyX 3067611 p.Lys112Thr missense_variant 0.67
thyA 3073892 c.579delC frameshift_variant 0.25
ald 3086694 c.-126C>A upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086951 c.132T>C synonymous_variant 0.5
ald 3087121 p.Arg101Leu missense_variant 0.5
ald 3087570 p.Ser251Pro missense_variant 0.18
fbiD 3338931 c.-187C>T upstream_gene_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475058 p.Ser351Ile missense_variant 0.29
whiB7 3568814 c.-135T>A upstream_gene_variant 0.4
whiB7 3568871 c.-192C>A upstream_gene_variant 0.4
Rv3236c 3613182 c.-66T>G upstream_gene_variant 0.29
fbiB 3641903 c.369C>T synonymous_variant 1.0
fbiB 3642330 p.Phe266Ile missense_variant 0.5
fbiB 3642679 p.Gln382Leu missense_variant 0.5
fbiB 3642779 c.1245A>T synonymous_variant 0.25
ddn 3986699 c.-145C>A upstream_gene_variant 0.25
ddn 3986749 c.-95C>A upstream_gene_variant 0.29
clpC1 4038319 p.Pro796Thr missense_variant 0.4
clpC1 4038491 c.2214C>T synonymous_variant 0.33
clpC1 4038518 c.2187G>T synonymous_variant 0.33
clpC1 4038641 p.Asn688Lys missense_variant 1.0
clpC1 4039552 c.1153C>T synonymous_variant 0.33
clpC1 4040741 c.-37G>A upstream_gene_variant 0.29
clpC1 4040855 c.-151G>T upstream_gene_variant 0.25
panD 4044095 p.Glu63* stop_gained 0.5
panD 4044341 c.-61delT upstream_gene_variant 0.5
embC 4239879 p.Ala6Gly missense_variant 0.5
embC 4240172 p.Val104Met missense_variant 1.0
embC 4242058 c.2196G>T synonymous_variant 0.33
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244453 c.1221G>A synonymous_variant 0.67
embA 4246032 p.Pro934Ser missense_variant 0.4
embB 4247397 p.Ala295Glu missense_variant 0.22
embB 4247526 p.Ala338Val missense_variant 0.4
embB 4247532 p.Met340Thr missense_variant 0.33
embB 4248515 p.Val668Phe missense_variant 0.33
embB 4248744 p.Val744Asp missense_variant 0.33
embB 4248847 c.2334C>A synonymous_variant 0.18
aftB 4266985 p.Pro618Thr missense_variant 0.43
aftB 4267782 p.Val352Gly missense_variant 0.29
aftB 4268030 c.807G>A synonymous_variant 0.25
aftB 4269066 c.-230C>A upstream_gene_variant 0.4
ubiA 4269142 p.Leu231* stop_gained 0.43
ubiA 4269268 p.Ala189Val missense_variant 0.33
ethR 4327231 c.-318G>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0