TB-Profiler result

Run: ERR4830868
Summary

Run ID: ERR4830868

Sample name:

Date: 01-04-2023 20:30:33

Number of reads: 1740533

Percentage reads mapped: 95.48

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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
rpoB 761277 p.Ile491Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2289091 p.His51Asp missense_variant 1.0 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 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.27
rpoC 766467 p.Glu1033Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
mmpR5 779426 p.Met146Thr 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 1472956 n.1111T>C non_coding_transcript_exon_variant 0.11
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.12
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.12
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.12
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.11
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.13
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.14
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 0.15
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.12
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.14
rrl 1474660 n.1003G>A non_coding_transcript_exon_variant 0.15
rrl 1474673 n.1016T>G 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 0.42
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.33
rrl 1474717 n.1060_1061insGCCAG non_coding_transcript_exon_variant 0.31
rrl 1474752 n.1096delA non_coding_transcript_exon_variant 0.24
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.24
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.24
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.24
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.24
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.14
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.12
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.11
rrl 1475044 n.1387G>A non_coding_transcript_exon_variant 0.25
rrl 1475069 n.1412G>T non_coding_transcript_exon_variant 0.25
rrl 1475369 n.1712G>A non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518496 c.382C>T synonymous_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.17
Rv2752c 3065023 p.Pro390Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448522 p.Val7Phe missense_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.45
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246584 p.Arg24Pro missense_variant 0.14
embB 4248324 p.Ala604Gly missense_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0