TB-Profiler result

Run: ERR1213931
Summary

Run ID: ERR1213931

Sample name:

Date: 31-03-2023 12:44:46

Number of reads: 4448604

Percentage reads mapped: 97.81

Strain: lineage4.6.1.2;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 0.91
lineage4.6 Euro-American T;LAM None 0.09
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.86
lineage4.6.1.2 Euro-American T2 RD724 0.05
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 761155 p.Ser450Leu missense_variant 0.96 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288805 p.Ala146Val missense_variant 0.11 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.15 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 8040 p.Gly247Ser missense_variant 0.92
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 0.97
rpoC 766203 p.Gly945Val missense_variant 0.88
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461149 c.105T>G synonymous_variant 0.12
atpE 1461158 c.114T>C synonymous_variant 0.12
atpE 1461161 c.117C>T synonymous_variant 0.17
atpE 1461167 c.123G>C synonymous_variant 0.11
atpE 1461197 c.153A>G synonymous_variant 0.13
atpE 1461219 c.175T>C synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472035 n.190G>T non_coding_transcript_exon_variant 0.14
rrs 1472042 n.197T>C non_coding_transcript_exon_variant 0.11
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.14
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.28
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.31
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.33
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.25
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.24
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.24
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.23
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.23
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.12
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.13
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.2
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.22
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.23
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.18
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.15
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.27
rrl 1474841 n.1184G>T non_coding_transcript_exon_variant 0.18
rrl 1475315 n.1658A>C non_coding_transcript_exon_variant 0.12
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.12
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.23
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.23
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.19
rrl 1475446 n.1789G>C non_coding_transcript_exon_variant 0.18
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.15
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.12
rrl 1475760 n.2103C>T non_coding_transcript_exon_variant 0.13
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.11
rrl 1476108 n.2451T>C non_coding_transcript_exon_variant 0.1
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.12
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.11
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.16
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.24
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.2
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156490 c.-379G>C upstream_gene_variant 0.12
PPE35 2169320 p.Leu431Phe missense_variant 0.42
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.9
kasA 2519332 c.1218C>A synonymous_variant 0.21
ribD 2987307 p.Ala157Pro missense_variant 0.2
thyA 3073806 c.666C>G synonymous_variant 0.47
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.94
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.87
clpC1 4038857 c.1848C>A synonymous_variant 0.23
embC 4241146 c.1284C>G synonymous_variant 0.1
embC 4241162 c.1300T>C synonymous_variant 0.11
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407973 p.Val77Gly missense_variant 0.86
gid 4408156 p.Leu16Arg missense_variant 0.81