TB-Profiler result

Run: ERR2517074
Summary

Run ID: ERR2517074

Sample name:

Date: 19-10-2023 23:26:58

Number of reads: 3119275

Percentage reads mapped: 91.15

Strain: lineage3

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.Ile491Thr (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA c.470_471insA (1.00), pncA c.470_471insA (1.00)
Streptomycin
Fluoroquinolones R gyrA p.Ser91Pro (1.00)
Moxifloxacin R gyrA p.Ser91Pro (1.00)
Ofloxacin R gyrA p.Ser91Pro (1.00)
Levofloxacin R gyrA p.Ser91Pro (1.00)
Ciprofloxacin R gyrA p.Ser91Pro (1.00)
Aminoglycosides R rrs n.1402C>A (0.12)
Amikacin R rrs n.1402C>A (0.12)
Capreomycin R rrs n.1402C>A (0.12)
Kanamycin R rrs n.1402C>A (0.12)
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 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
gyrA 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 1.0 rifampicin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.12 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288771 c.470_471insA frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4247431 p.Met306Ile 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 8948 c.1647G>A synonymous_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764644 c.1275G>C synonymous_variant 0.1
rpoC 764650 c.1281G>T synonymous_variant 0.12
rpoC 764662 c.1293G>C synonymous_variant 0.12
rpoC 764677 c.1308C>G synonymous_variant 0.12
rpoC 764731 c.1362G>C synonymous_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.13
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.13
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.13
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.15
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.14
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.18
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.16
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.17
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.17
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.17
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.17
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.17
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.16
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.18
rrs 1473127 n.1282G>A non_coding_transcript_exon_variant 0.17
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.16
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.11
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.12
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.12
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.12
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.13
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.12
rrl 1474660 n.1003G>A non_coding_transcript_exon_variant 0.14
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.15
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.14
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.15
rrl 1474690 n.1033C>T non_coding_transcript_exon_variant 0.16
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.14
rrl 1474717 n.1060_1061insGTGAG non_coding_transcript_exon_variant 0.14
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.16
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.16
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.14
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.15
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.16
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.29
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.29
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.3
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.3
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.3
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.28
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.2
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.22
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.22
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.22
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.19
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.19
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.18
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.18
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.17
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.16
rrl 1476422 n.2765C>G non_coding_transcript_exon_variant 0.14
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.14
rrl 1476430 n.2773G>T non_coding_transcript_exon_variant 0.14
rrl 1476431 n.2774G>C non_coding_transcript_exon_variant 0.14
rpsA 1833979 c.438T>C synonymous_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A 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
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249606 c.3093C>T synonymous_variant 0.99
ubiA 4269908 c.-75C>G upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408124 p.Ala27Pro missense_variant 1.0