TB-Profiler result

Run: ERR4829196
Summary

Run ID: ERR4829196

Sample name:

Date: 01-04-2023 19:20:32

Number of reads: 3164280

Percentage reads mapped: 50.16

Strain: lineage4.1.2

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
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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.12 kanamycin, capreomycin, aminoglycosides, amikacin
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 7623 p.Pro108Thr missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.18
mshA 576412 p.Phe355Leu missense_variant 0.11
mshA 576615 p.Arg423Pro missense_variant 0.11
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761234 c.1428G>C synonymous_variant 0.16
rpoB 761235 p.Met477Val missense_variant 0.16
rpoB 761258 c.1452G>A synonymous_variant 0.12
rpoB 762218 c.2412T>C synonymous_variant 0.16
rpoB 762225 p.Glu807Gln missense_variant 0.1
rpoB 762228 c.2422C>T synonymous_variant 0.11
rpoB 762254 c.2448T>C synonymous_variant 0.1
rpoB 762257 c.2451C>G synonymous_variant 0.1
rpoB 762888 p.His1028Asn missense_variant 0.12
rpoB 762911 p.Ile1035Met missense_variant 0.12
rpoC 762920 c.-450C>T upstream_gene_variant 0.12
rpoC 762929 c.-441G>C upstream_gene_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776659 p.Asp608Asn missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.22
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 0.17
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.19
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.12
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.31
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.12
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.24
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.16
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.16
rrs 1472374 n.529T>A non_coding_transcript_exon_variant 0.2
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.31
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.29
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.29
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.28
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.23
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.2
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.11
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.14
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.36
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.38
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.4
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.32
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.32
rrs 1472827 n.982G>C non_coding_transcript_exon_variant 0.23
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.23
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.25
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.26
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.13
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.36
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.32
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.31
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.33
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.27
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.18
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.14
rrs 1473097 n.1252G>C non_coding_transcript_exon_variant 0.13
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.12
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.16
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155896 c.216C>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.45
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568437 c.243T>C synonymous_variant 0.21
rpoA 3878557 c.-50G>A upstream_gene_variant 0.29
clpC1 4039685 c.1020C>G synonymous_variant 0.11
clpC1 4040033 c.672G>C synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0