TB-Profiler result

Run: ERR027451
Summary

Run ID: ERR027451

Sample name:

Date: 20-10-2023 23:28:14

Number of reads: 3624715

Percentage reads mapped: 97.78

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (1.00), rpoC p.Asp485Asn (1.00)
Isoniazid R inhA c.-154G>A (0.62), katG p.Ile335Val (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Gln497Arg (1.00)
Pyrazinamide R pncA p.Thr135Pro (0.97)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrA p.Asp94Gly (0.95)
Moxifloxacin R gyrA p.Asp94Gly (0.95)
Ofloxacin R gyrA p.Asp94Gly (0.95)
Levofloxacin R gyrA p.Asp94Gly (0.95)
Ciprofloxacin R gyrA p.Asp94Gly (0.95)
Aminoglycosides R rrs n.1401A>G (0.97)
Amikacin R rrs n.1401A>G (0.97)
Capreomycin R rrs n.1401A>G (0.97)
Kanamycin R rrs n.1401A>G (0.97)
Cycloserine
Ethionamide R inhA c.-154G>A (0.62)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrA 7582 p.Asp94Gly missense_variant 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764822 p.Asp485Asn missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.97 kanamycin, capreomycin, aminoglycosides, amikacin
inhA 1674048 c.-154G>A upstream_gene_variant 0.62 isoniazid, ethionamide
katG 2155109 p.Ile335Val missense_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288839 p.Thr135Pro missense_variant 0.97 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.97
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.94
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302917 c.-14_-13insA upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.22
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.36
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.41
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.43
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.6
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.49
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.42
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.35
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.19
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.3
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.29
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.31
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.24
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.24
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.3
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.37
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.4
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.42
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.44
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.48
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.44
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.36
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.36
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.39
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.46
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.46
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.43
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.4
rrs 1473080 n.1235C>A non_coding_transcript_exon_variant 0.22
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.3
rrs 1473201 n.1356_1357delACinsT non_coding_transcript_exon_variant 0.34
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.34
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.16
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.3
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.2
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.2
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.2
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.23
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.21
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.22
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.23
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.26
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.39
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.44
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.35
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.31
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.33
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.38
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.49
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.44
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.42
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.46
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.41
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.37
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.37
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.51
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.41
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834776 p.Ala412Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640879 c.-656C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243598 c.366G>A synonymous_variant 1.0
embB 4247872 c.1359C>T synonymous_variant 1.0
ethA 4326474 p.Pro334Ala missense_variant 1.0
whiB6 4338326 p.Ala66Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0