TB-Profiler result

Run: ERR4820100
Summary

Run ID: ERR4820100

Sample name:

Date: 01-04-2023 16:28:58

Number of reads: 869628

Percentage reads mapped: 78.5

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 0.61 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 6572 p.Cys445Arg missense_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8555 c.1254G>A synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576738 p.Val464Ala missense_variant 0.11
rpoB 762237 p.Glu811* stop_gained 0.11
rpoC 763597 c.228G>A synonymous_variant 0.11
rpoC 763598 p.Arg77Lys missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 767000 p.Thr1211Ala missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777086 p.Ile465Met missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416797 p.Cys184Phe missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.2
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.14
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.26
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.11
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.17
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 0.11
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.19
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.3
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.3
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.43
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.53
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.54
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.54
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.54
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.51
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.51
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.53
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.52
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.52
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.5
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.21
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.32
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.37
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.57
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.57
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.49
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.48
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.17
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.16
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.14
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.14
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.11
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.14
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.14
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.12
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.12
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.11
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.11
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.1
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.18
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.21
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.26
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.16
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.12
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.11
rrl 1473961 n.304G>A non_coding_transcript_exon_variant 0.2
rrl 1475707 n.2050T>C non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.18
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.18
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.18
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.14
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.14
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.14
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.11
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.2
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.22
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.13
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.22
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.22
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.17
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.22
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.2
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.2
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.29
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.23
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.12
inhA 1674368 p.Ala56Glu missense_variant 0.14
rpsA 1833371 c.-171G>A upstream_gene_variant 0.13
rpsA 1834363 c.822G>A synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168540 c.2073C>A synonymous_variant 0.11
Rv1979c 2222182 p.Thr328Asn missense_variant 0.2
Rv1979c 2222994 c.171C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289694 c.-453G>A upstream_gene_variant 0.11
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714832 c.501A>G synonymous_variant 0.11
eis 2715120 c.213G>A synonymous_variant 1.0
thyX 3067479 p.Asp156Gly missense_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339426 c.309T>C synonymous_variant 0.17
Rv3083 3448437 c.-67C>A upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640849 p.Glu103Lys missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243191 c.-42C>G upstream_gene_variant 0.1
embA 4243213 c.-20G>A upstream_gene_variant 0.1
embB 4248817 p.Asp768Glu missense_variant 0.11
embB 4249328 p.Met939Val missense_variant 1.0
embB 4249703 c.3190C>T synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408279 c.-77G>A upstream_gene_variant 0.11