TB-Profiler result

Run: ERR4818834
Summary

Run ID: ERR4818834

Sample name:

Date: 01-04-2023 15:46:37

Number of reads: 1232615

Percentage reads mapped: 97.49

Strain: lineage4.1.2.1

Drug-resistance: Other

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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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gid 4408100 c.102delG frameshift_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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 759801 c.-6T>C upstream_gene_variant 0.11
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760524 p.Glu240Lys missense_variant 0.1
rpoC 763462 c.93G>C synonymous_variant 0.11
rpoC 763486 c.117T>C synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777064 p.Phe473Ile missense_variant 0.12
mmpL5 778372 c.106_108delATC conservative_inframe_deletion 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781892 c.333A>G synonymous_variant 0.11
fbiC 1304912 c.1984delG frameshift_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.17
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.15
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.1
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.11
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.11
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.11
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.1
rrs 1472973 n.1128A>C non_coding_transcript_exon_variant 0.12
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.11
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.12
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.11
rrl 1474084 n.431delA non_coding_transcript_exon_variant 0.22
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.1
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.15
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.15
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.14
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.14
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.14
rrl 1475765 n.2108A>C non_coding_transcript_exon_variant 0.14
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.14
rrl 1475908 n.2251A>T non_coding_transcript_exon_variant 0.11
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.11
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.11
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.21
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168041 p.Ala858Thr missense_variant 0.17
Rv1979c 2222644 p.Leu174Pro missense_variant 0.14
Rv1979c 2222797 p.Pro123Leu missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726253 p.Gly21Ser missense_variant 0.12
Rv2752c 3065025 c.1167G>A synonymous_variant 0.13
Rv2752c 3065898 c.294C>A synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840444 p.Leu326Arg missense_variant 0.18
rpoA 3877476 c.1032C>A synonymous_variant 0.13
rpoA 3877727 c.780dupC frameshift_variant 0.12
rpoA 3878253 c.255G>T synonymous_variant 0.12
rpoA 3878362 p.Ala49Val missense_variant 0.11
clpC1 4038672 c.2030_2032delTCG disruptive_inframe_deletion 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4248379 c.1866G>A synonymous_variant 0.22
aftB 4266960 p.Arg626Leu missense_variant 0.12
aftB 4268234 c.603G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0