TB-Profiler result

Run: ERR2229184
Summary

Run ID: ERR2229184

Sample name:

Date: 31-03-2023 16:47:16

Number of reads: 600202

Percentage reads mapped: 99.58

Strain: lineage4.8

Drug-resistance: Sensitive

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
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 8229 p.Val310Phe missense_variant 0.12
gyrA 9184 p.Arg628Leu missense_variant 0.13
fgd1 491239 p.Asp153Asn missense_variant 0.25
fgd1 491441 p.Arg220Leu missense_variant 0.14
ccsA 620461 p.Val191Phe missense_variant 0.13
rpoB 761152 p.Leu449Gln missense_variant 0.15
rpoB 762192 p.Leu796Met missense_variant 0.12
rpoC 763940 p.Ala191Ser missense_variant 0.12
rpoC 764970 p.Ala534Asp missense_variant 0.12
rpoC 765447 p.Gln693Arg missense_variant 0.18
rpoC 766905 p.Ser1179Trp missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775883 p.Ile866Leu missense_variant 0.17
mmpL5 775927 c.2554C>T synonymous_variant 0.17
mmpL5 775931 c.2550C>T synonymous_variant 0.17
mmpL5 776250 p.Glu744Gly missense_variant 0.13
mmpL5 777157 c.1324C>A synonymous_variant 0.17
mmpL5 777164 c.1317C>T synonymous_variant 0.14
mmpS5 778770 p.Asp46Asn missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781562 c.3G>A start_lost 0.12
rplC 801374 p.Asn189Ser missense_variant 0.11
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304433 c.1503G>T synonymous_variant 0.18
embR 1416820 c.528C>A synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473207 n.1362C>A non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474144 n.487G>T non_coding_transcript_exon_variant 0.22
rrl 1476338 n.2681C>A non_coding_transcript_exon_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31
rpsA 1833448 c.-94G>A upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.19
PPE35 2169272 c.1341C>G synonymous_variant 0.19
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2170518 p.Asp32Thr missense_variant 0.11
PPE35 2170540 c.73C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518647 p.Ile178Asn missense_variant 0.2
kasA 2519140 c.1026G>C synonymous_variant 0.43
kasA 2519143 c.1029G>C synonymous_variant 0.43
eis 2714377 p.Thr319Met missense_variant 0.12
pepQ 2859671 p.Tyr250Asn missense_variant 0.4
Rv3236c 3612743 p.Thr125Asn missense_variant 0.13
fbiA 3640457 c.-86G>T upstream_gene_variant 0.12
fbiB 3641916 p.Ser128Gly missense_variant 0.29
clpC1 4038986 p.Asp573Glu missense_variant 0.13
clpC1 4039101 p.Thr535Asn missense_variant 0.12
clpC1 4039645 p.His354Asp missense_variant 0.15
clpC1 4040144 c.561G>C synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244560 p.Ile443Asn missense_variant 0.22
embA 4246089 p.Trp953Arg missense_variant 0.12
embB 4247470 c.957T>C synonymous_variant 0.22
embB 4247472 p.Phe320Tyr missense_variant 0.22
embB 4248227 p.Trp572Arg missense_variant 0.11
ethR 4326961 c.-588G>C upstream_gene_variant 0.14
ethR 4326964 c.-585G>A upstream_gene_variant 0.14
ethR 4326970 c.-579G>T upstream_gene_variant 0.15
ethR 4326982 c.-567C>G upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0