TB-Profiler result

Run: ERR4830856

Summary

Run ID: ERR4830856

Sample name:

Date: 01-04-2023 20:29:51

Number of reads: 2118127

Percentage reads mapped: 80.01

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 0.99 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.11 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 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 0.35
mshA 576113 p.Arg256Gly missense_variant 0.16
rpoC 764503 c.1134G>C synonymous_variant 0.1
rpoC 764521 c.1152T>C synonymous_variant 0.13
rpoC 764536 c.1167G>T synonymous_variant 0.14
rpoC 764539 c.1170C>G synonymous_variant 0.15
rpoC 764542 c.1173C>G synonymous_variant 0.14
rpoC 764545 c.1176C>G synonymous_variant 0.19
rpoC 764548 c.1179G>C synonymous_variant 0.18
rpoC 764560 c.1191T>C synonymous_variant 0.18
rpoC 764572 c.1203G>C synonymous_variant 0.17
rpoC 764573 p.Leu402Ile missense_variant 0.14
rpoC 764578 c.1209C>G synonymous_variant 0.14
rpoC 764581 c.1212T>C synonymous_variant 0.16
rpoC 764582 p.Leu405Met missense_variant 0.16
rpoC 764611 c.1242G>C synonymous_variant 0.13
rpoC 764632 c.1263T>C synonymous_variant 0.1
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 1472172 n.327T>C non_coding_transcript_exon_variant 0.11
rrs 1472686 n.841G>A non_coding_transcript_exon_variant 0.11
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.12
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.12
rrl 1473981 n.324G>T non_coding_transcript_exon_variant 0.22
rrl 1474068 n.411T>A non_coding_transcript_exon_variant 0.12
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.12
rrl 1474281 n.624A>G non_coding_transcript_exon_variant 0.11
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 0.1
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.12
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.12
rrl 1474359 n.702C>G non_coding_transcript_exon_variant 0.12
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.12
rrl 1474381 n.724T>A non_coding_transcript_exon_variant 0.14
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.16
rrl 1474402 n.745T>C non_coding_transcript_exon_variant 0.12
rrl 1474450 n.793T>A non_coding_transcript_exon_variant 0.12
rrl 1474454 n.797G>A non_coding_transcript_exon_variant 0.12
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.14
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.11
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.11
rrl 1474630 n.973T>C non_coding_transcript_exon_variant 0.11
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.14
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.11
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.12
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.12
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.12
rrl 1474660 n.1003G>A non_coding_transcript_exon_variant 0.25
rrl 1474673 n.1016T>G non_coding_transcript_exon_variant 0.18
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.22
rrl 1474690 n.1033C>T non_coding_transcript_exon_variant 0.23
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.26
rrl 1474717 n.1060_1061insGCCAG non_coding_transcript_exon_variant 0.22
rrl 1474752 n.1096delA non_coding_transcript_exon_variant 0.27
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.28
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.3
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.24
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.26
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.15
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.12
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.12
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.13
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.13
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.13
rrl 1475086 n.1429C>A non_coding_transcript_exon_variant 0.13
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.23
rrl 1475776 n.2119G>C non_coding_transcript_exon_variant 0.23
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.14
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.14
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.15
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.15
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.15
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.15
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.17
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.2
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.16
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.12
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.27
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.26
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.24
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.18
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.15
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
Rv2752c 3065023 p.Pro390Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.56
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 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
embA 4244910 c.1678C>T synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0