TB-Profiler result

Run: ERR1213928
Summary

Run ID: ERR1213928

Sample name:

Date: 31-03-2023 12:45:11

Number of reads: 4280424

Percentage reads mapped: 98.59

Strain: lineage4.3.3

Drug-resistance: MDR-TB

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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 0.98
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.97
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
rpoB 761110 p.Asp435Val missense_variant 0.93 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 1.0 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 0.96 ethambutol
gid 4407952 p.Pro84Leu missense_variant 1.0 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
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 9300 p.Ala667Ser missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575984 c.637T>C synonymous_variant 0.11
mshA 576611 p.Ala422Thr missense_variant 0.13
rpoB 761015 c.1209G>C synonymous_variant 0.17
rpoB 761027 c.1221A>G synonymous_variant 0.12
rpoB 761037 c.1231T>C synonymous_variant 0.15
rpoB 761051 c.1245G>T synonymous_variant 0.12
rpoC 764207 p.Val280Ile missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765886 c.2517C>G synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777494 c.987G>T synonymous_variant 0.12
mmpL5 777511 c.970C>T synonymous_variant 0.13
mmpL5 777512 c.969T>C synonymous_variant 0.13
mmpL5 777518 c.963G>C synonymous_variant 0.12
mmpL5 777527 c.954G>C synonymous_variant 0.14
mmpL5 777533 c.948C>G synonymous_variant 0.13
mmpL5 777542 c.939G>A synonymous_variant 0.13
mmpL5 777563 c.918C>G synonymous_variant 0.2
mmpL5 777587 c.894G>C synonymous_variant 0.12
mmpL5 778807 c.-327T>G upstream_gene_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305315 c.2385C>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471969 n.124T>C non_coding_transcript_exon_variant 0.1
rrs 1472035 n.190G>T non_coding_transcript_exon_variant 0.19
rrs 1472042 n.197T>C non_coding_transcript_exon_variant 0.16
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.12
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.13
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.31
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.45
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.52
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.53
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.5
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.26
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.26
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.27
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.2
rrl 1473924 n.267_268insT non_coding_transcript_exon_variant 0.2
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.14
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.17
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.18
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.17
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.18
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.22
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.17
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.21
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.2
rrl 1474957 n.1301delA non_coding_transcript_exon_variant 0.14
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.17
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.3
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.31
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.27
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.2
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.14
rrl 1475446 n.1789G>C non_coding_transcript_exon_variant 0.13
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.15
rrl 1475760 n.2103C>T non_coding_transcript_exon_variant 0.16
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.13
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.17
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.12
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.11
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.14
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.22
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.17
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.15
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.15
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.16
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.14
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.31
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.29
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.2
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.28
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.32
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.2
rrl 1476692 n.3035T>A non_coding_transcript_exon_variant 0.12
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.12
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.25
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.18
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.88
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168998 p.Ile539Val missense_variant 0.98
PPE35 2169320 p.Leu431Phe missense_variant 0.46
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746228 c.1371C>A synonymous_variant 0.17
thyX 3067886 c.60A>C synonymous_variant 0.11
thyX 3067898 p.Asp16Glu missense_variant 0.11
thyX 3067916 c.30A>G synonymous_variant 0.1
thyA 3073806 c.666C>G synonymous_variant 0.26
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.96
fbiD 3339153 p.Leu12Phe missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.12
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326823 p.Asp217Glu missense_variant 0.13
ethA 4328234 c.-761T>G upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0