TB-Profiler result

Run: ERR757150
Summary

Run ID: ERR757150

Sample name:

Date: 02-04-2023 05:05:22

Number of reads: 1857455

Percentage reads mapped: 98.98

Strain: lineage4.1.2.1.1

Drug-resistance: MDR-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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 0.98
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 1.0
lineage4.1.2.1.1 Euro-American (Haarlem) T1;H1 RD182 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288815 p.Ala143Thr missense_variant 0.18 pyrazinamide
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
gid 4407872 c.329_330delTG frameshift_variant 1.0 streptomycin
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 6448 c.-854G>A upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7472 p.Tyr57* stop_gained 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7591 p.Val97Glu missense_variant 0.15
gyrA 8413 p.Asp371Gly missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.94
mshA 575448 p.Ser34Phe missense_variant 0.12
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575683 c.336G>A synonymous_variant 0.14
mshA 575970 p.Asp208Gly missense_variant 0.11
mshA 576574 c.1227T>C synonymous_variant 0.17
ccsA 620537 p.Val216Gly missense_variant 0.19
rpoB 759615 c.-192A>C upstream_gene_variant 0.33
rpoB 759620 c.-187A>C upstream_gene_variant 0.4
rpoB 759990 p.Pro62Ser missense_variant 0.14
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761043 p.Asn413Asp missense_variant 0.12
rpoB 762293 c.2487T>A synonymous_variant 0.22
rpoC 764296 c.927G>A synonymous_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766167 p.Ala933Val missense_variant 0.33
rpoC 766232 p.Ala955Thr missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777103 p.Ala460Thr missense_variant 0.17
mmpL5 777332 c.1149G>A synonymous_variant 0.22
mmpL5 777793 p.Ala230Thr missense_variant 1.0
mmpR5 779318 p.Ala110Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781722 p.Val55Met missense_variant 0.12
fbiC 1303489 c.559C>T synonymous_variant 0.12
Rv1258c 1407522 c.-182C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472576 n.731T>A non_coding_transcript_exon_variant 0.12
rrs 1473039 n.1194T>C non_coding_transcript_exon_variant 0.13
rrs 1473278 n.1433T>A non_coding_transcript_exon_variant 0.12
rrl 1474803 n.1146G>T non_coding_transcript_exon_variant 0.12
fabG1 1673339 c.-101C>G upstream_gene_variant 0.1
fabG1 1674107 p.Phe223Tyr missense_variant 0.12
rpsA 1834760 p.Phe407Leu missense_variant 0.11
rpsA 1834914 c.1374G>A synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918600 p.His221Tyr missense_variant 0.17
tlyA 1918622 p.Ser228Asn missense_variant 0.14
ndh 2102012 p.Ala344Val missense_variant 0.12
ndh 2103118 c.-76T>C upstream_gene_variant 0.14
katG 2155670 c.442C>T synonymous_variant 0.18
PPE35 2169133 p.Ala494Thr missense_variant 0.12
PPE35 2169751 p.Gly288* stop_gained 1.0
PPE35 2169806 c.807T>C synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288858 c.384C>T synonymous_variant 0.11
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518435 c.321G>A synonymous_variant 0.12
ahpC 2726019 c.-174C>T upstream_gene_variant 0.12
ahpC 2726063 c.-130C>T upstream_gene_variant 0.14
ahpC 2726338 p.Val49Gly missense_variant 0.41
ahpC 2726341 p.Val50Gly missense_variant 0.28
ahpC 2726350 p.Trp53Leu missense_variant 0.31
folC 2747750 c.-152G>A upstream_gene_variant 0.12
Rv2752c 3064995 c.1197C>A synonymous_variant 0.11
thyX 3067500 p.Lys149Met missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087281 c.462G>A synonymous_variant 0.14
Rv3083 3448707 c.204G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3640578 c.-957C>T upstream_gene_variant 0.11
fbiA 3641447 p.Thr302Met missense_variant 0.18
fbiB 3642708 p.Gly392Trp missense_variant 0.13
alr 3840827 c.594T>C synonymous_variant 0.15
rpoA 3877514 p.Thr332Ala missense_variant 0.11
rpoA 3878706 c.-199G>C upstream_gene_variant 0.11
ddn 3986706 c.-138A>G upstream_gene_variant 0.11
clpC1 4038804 p.Ile634Asn missense_variant 0.12
clpC1 4039637 c.1068C>T synonymous_variant 0.17
clpC1 4039858 p.Ile283Phe missense_variant 0.12
embC 4241055 c.1194_1195delCG frameshift_variant 0.12
embC 4241093 p.Cys411Ser missense_variant 0.13
embC 4241097 p.Ser412Leu missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246223 c.-291C>T upstream_gene_variant 0.11
embB 4247179 c.666C>T synonymous_variant 0.25
embB 4247837 c.1324C>T synonymous_variant 0.2
embB 4247905 c.1392G>T synonymous_variant 0.15
aftB 4268940 c.-104T>C upstream_gene_variant 0.13
aftB 4269027 c.-191C>T upstream_gene_variant 0.13
ubiA 4269109 p.Gly242Asp missense_variant 0.12
ethR 4328159 p.Val204Glu missense_variant 0.11
ethA 4328200 c.-727C>T upstream_gene_variant 0.11
ethA 4328356 c.-883C>T upstream_gene_variant 0.22
whiB6 4338326 p.Ala66Thr missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407717 c.486C>T synonymous_variant 0.11
gid 4408007 p.Val66Met missense_variant 0.12