TB-Profiler result

Run: ERR245801
Summary

Run ID: ERR245801

Sample name:

Date: 31-03-2023 18:22:32

Number of reads: 17470742

Percentage reads mapped: 61.09

Strain: lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 0.99
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.99
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 0.51 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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.24
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620407 p.Pro173Ala missense_variant 0.27
rpoB 759831 p.Thr9Pro missense_variant 0.22
rpoB 762249 p.Leu815Val missense_variant 0.16
rpoC 762836 c.-534C>G upstream_gene_variant 0.21
rpoC 764995 c.1626C>G synonymous_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417501 c.-154A>C upstream_gene_variant 0.24
atpE 1461019 c.-26C>A upstream_gene_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.12
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.16
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.16
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.16
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.1
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.1
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.2
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.27
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.28
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.41
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.44
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.45
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.45
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.54
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.53
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.48
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.48
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.36
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.36
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.29
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.22
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.37
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.38
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.54
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.55
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.49
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.45
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.37
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.11
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.29
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.33
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.33
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.33
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.33
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.18
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.23
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.25
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.26
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.25
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.24
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.21
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.21
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.16
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.27
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.27
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.29
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.29
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.14
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.19
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.26
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.37
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.4
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.43
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.44
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.48
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.48
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.52
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.5
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.5
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.43
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.18
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.12
fabG1 1673449 p.Thr4Pro missense_variant 0.31
inhA 1674892 p.Asn231Asp missense_variant 0.2
rpsA 1833422 c.-120G>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.21
PPE35 2167871 c.2742G>C synonymous_variant 0.22
PPE35 2169320 p.Leu431Phe missense_variant 0.16
PPE35 2169379 p.Phe412Val missense_variant 0.21
PPE35 2169866 c.747G>C synonymous_variant 0.35
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.24
eis 2715586 c.-254G>C upstream_gene_variant 0.57
ahpC 2725954 c.-239C>T upstream_gene_variant 0.32
pepQ 2859381 c.1038C>G synonymous_variant 0.18
Rv2752c 3064741 p.Gly484Ala missense_variant 0.3
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Gly missense_variant 0.25
Rv3236c 3612009 p.Ala370Thr missense_variant 0.99
fbiB 3641955 p.Gly141Arg missense_variant 0.25
fbiB 3642734 c.1200G>C synonymous_variant 0.3
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039363 p.Ala448Pro missense_variant 0.29
clpC1 4039932 p.Gly258Val missense_variant 0.28
embC 4241056 c.1194C>G synonymous_variant 0.27
embC 4241429 p.Phe523Val missense_variant 0.46
embC 4241456 p.Ala532Pro missense_variant 0.45
embC 4242476 p.Pro872Ala missense_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embC 4242822 p.Val987Gly missense_variant 0.37
embA 4243977 p.Ala249Pro missense_variant 0.34
ubiA 4269529 p.Ala102Gly missense_variant 0.18
ethA 4327672 c.-199G>A upstream_gene_variant 0.28
ethR 4327912 p.Arg122Gly missense_variant 0.23
whiB6 4338439 c.82dupG frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0