TB-Profiler result

Run: ERR4830864
Summary

Run ID: ERR4830864

Sample name:

Date: 01-04-2023 20:30:18

Number of reads: 2929497

Percentage reads mapped: 95.69

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 0.99 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.15 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289091 p.His51Asp missense_variant 0.99 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 0.98
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.26
mshA 576482 p.Val379Leu missense_variant 0.11
rpoC 766467 p.Glu1033Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 0.99
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 1472238 n.393G>T non_coding_transcript_exon_variant 0.13
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.1
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.12
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.12
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.15
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.16
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.16
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.16
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.16
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.16
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.16
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.16
rrl 1474529 n.872A>T non_coding_transcript_exon_variant 0.17
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.18
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.17
rrl 1474630 n.973T>C non_coding_transcript_exon_variant 0.17
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.16
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.16
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.16
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.2
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.16
rrl 1474660 n.1003G>A non_coding_transcript_exon_variant 0.18
rrl 1474673 n.1016T>G non_coding_transcript_exon_variant 0.15
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.14
rrl 1474690 n.1033C>T non_coding_transcript_exon_variant 0.12
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.11
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.11
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.11
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.12
rrl 1475076 n.1419C>T non_coding_transcript_exon_variant 0.12
rrl 1475757 n.2100A>C non_coding_transcript_exon_variant 0.3
rrl 1475759 n.2102C>G non_coding_transcript_exon_variant 0.3
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.36
rrl 1475776 n.2119G>C non_coding_transcript_exon_variant 0.27
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.11
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.11
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.11
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.11
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.11
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.16
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
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.18
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
fbiD 3339734 p.Ala206Gly missense_variant 0.17
fbiD 3339746 p.Ala210Gly missense_variant 0.27
Rv3083 3448522 p.Val7Phe missense_variant 0.99
Rv3083 3448608 c.105G>A synonymous_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
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 0.14
embB 4246555 c.42G>C synonymous_variant 0.11
embB 4246556 p.Ala15Pro missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0