TB-Profiler result

Run: ERR2510736
Summary

Run ID: ERR2510736

Sample name:

Date: 31-03-2023 18:54:42

Number of reads: 1115445

Percentage reads mapped: 72.84

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 0.98
lineage4.1.2.1 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.67 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
gyrB 6578 p.Ser447Pro missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8633 c.1332C>G synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491300 p.Tyr173Phe missense_variant 0.17
fgd1 491408 p.Pro209Arg missense_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576383 p.Val346Phe missense_variant 0.11
rpoB 759848 p.Ser14Arg missense_variant 0.12
rpoB 760106 c.300G>A synonymous_variant 0.94
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761501 c.1695G>T synonymous_variant 0.11
rpoB 762476 c.2672delA frameshift_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766313 p.Ser982Pro missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775971 p.Ala837Val missense_variant 0.11
mmpL5 776171 c.2310C>T synonymous_variant 0.12
mmpL5 778365 p.Trp39Leu missense_variant 0.13
mmpR5 779449 p.Leu154Met missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800712 c.-97A>G upstream_gene_variant 0.1
fbiC 1304326 c.1396C>T synonymous_variant 0.12
fbiC 1304673 c.1743C>T synonymous_variant 0.1
fbiC 1305061 p.Gly711Trp missense_variant 0.15
Rv1258c 1407232 p.Arg37Cys missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471866 n.21C>T non_coding_transcript_exon_variant 0.5
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.67
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 1.0
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 1.0
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 1.0
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.71
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.29
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 1.0
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 1.0
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 1.0
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.5
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.5
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.5
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.5
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.25
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.25
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 1.0
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 1.0
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 1.0
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.67
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.67
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.67
rrl 1474798 n.1141C>G non_coding_transcript_exon_variant 0.67
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.67
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.67
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.4
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.4
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.33
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.33
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.2
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.2
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.4
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.2
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.25
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.18
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.36
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.55
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.22
rrl 1476256 n.2599A>C non_coding_transcript_exon_variant 0.18
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.36
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.7
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.5
fabG1 1673380 c.-60C>G upstream_gene_variant 0.29
inhA 1673475 c.-727A>G upstream_gene_variant 0.2
fabG1 1673672 c.235delC frameshift_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103014 p.Gln10Arg missense_variant 0.1
katG 2153914 p.Asn733Ser missense_variant 0.13
katG 2154441 p.Lys557Asn missense_variant 1.0
PPE35 2168087 c.2525delC frameshift_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.33
PPE35 2170066 p.Ala183Thr missense_variant 0.25
PPE35 2170516 p.Gly33Trp missense_variant 0.22
Rv1979c 2222315 p.Ala284Thr missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289830 c.-589G>T upstream_gene_variant 0.2
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518470 p.Ala119Gly missense_variant 0.25
eis 2715380 c.-48G>T upstream_gene_variant 0.14
Rv2752c 3065360 p.Phe278Val missense_variant 0.15
Rv2752c 3065464 p.Asp243Val missense_variant 0.13
Rv2752c 3065896 p.Asp99Gly missense_variant 0.11
Rv2752c 3066160 p.Leu11Pro missense_variant 0.14
Rv2752c 3066178 p.Leu5Arg missense_variant 0.17
thyX 3067336 p.Ala204Thr missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448763 p.Asp87Val missense_variant 0.12
Rv3083 3449637 c.1134G>C synonymous_variant 0.17
Rv3083 3449865 p.Gln454His missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474887 p.Leu294Pro missense_variant 0.29
fprA 3475057 p.Ser351Cys missense_variant 0.15
fprA 3475094 p.Gly363Glu missense_variant 0.11
whiB7 3568540 p.Pro47Gln missense_variant 0.14
Rv3236c 3612242 p.Pro292Leu missense_variant 0.1
Rv3236c 3612761 p.Leu119His missense_variant 0.14
Rv3236c 3613062 p.Ala19Thr missense_variant 0.12
fbiA 3640657 p.His39Asp missense_variant 0.11
fbiA 3640711 p.Arg57Ser missense_variant 0.12
fbiA 3641252 p.Thr237Asn missense_variant 0.15
fbiB 3641679 p.Thr49Ala missense_variant 0.15
alr 3840909 p.Gln171Arg missense_variant 0.12
clpC1 4038818 c.1887G>A synonymous_variant 0.13
clpC1 4040213 c.492T>C synonymous_variant 0.2
embC 4239882 p.Pro7Arg missense_variant 0.15
embC 4240071 p.Val70Asp missense_variant 0.18
embC 4240087 c.225T>C synonymous_variant 0.2
embC 4240406 p.Ala182Thr missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244309 c.1077C>G synonymous_variant 0.17
embA 4244502 p.Gln424* stop_gained 0.25
embA 4246159 p.Pro976Gln missense_variant 0.12
embA 4246416 c.3186delG frameshift_variant 0.2
embB 4247498 p.Pro329Thr missense_variant 0.12
aftB 4267596 p.Tyr414Cys missense_variant 0.12
aftB 4268016 p.Val274Ala missense_variant 1.0
ubiA 4268972 p.Ala288Ser missense_variant 0.12
ethA 4326036 p.Phe480Leu missense_variant 0.12
ethA 4326960 p.Asp172Asn missense_variant 0.18
whiB6 4338218 p.Asn102Asp missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408011 c.192G>A synonymous_variant 0.15
gid 4408021 p.Arg61His missense_variant 0.18
gid 4408274 c.-72G>A upstream_gene_variant 0.11