TB-Profiler result

Run: ERR2229510

Summary

Run ID: ERR2229510

Sample name:

Date: 31-03-2023 17:16:32

Number of reads: 1135964

Percentage reads mapped: 98.98

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
mshA 576108 p.Ala254Gly missense_variant 0.16
rpoB 759925 p.Glu40Gly missense_variant 0.12
rpoB 762787 p.Val994Ala missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775774 p.Met903Leu missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303807 p.Gln293Lys missense_variant 0.17
fbiC 1304876 p.Ile649Thr missense_variant 0.12
Rv1258c 1406933 c.408C>A synonymous_variant 0.12
embR 1416982 c.366C>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474025 n.368T>A non_coding_transcript_exon_variant 0.33
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
rpsA 1834246 c.705G>T synonymous_variant 0.11
rpsA 1834383 p.Glu281Gly missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.14
PPE35 2169910 p.Asn235Tyr missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.27
PPE35 2170053 p.Thr187Ser missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518729 c.615G>T synonymous_variant 0.14
kasA 2519140 c.1026G>C synonymous_variant 0.2
kasA 2519143 c.1029G>C synonymous_variant 0.22
kasA 2519329 c.1215C>T synonymous_variant 0.18
eis 2714993 p.Pro114Ala missense_variant 0.17
Rv2752c 3065439 c.753C>T synonymous_variant 0.12
Rv2752c 3067173 c.-982A>G upstream_gene_variant 0.12
thyX 3067886 c.59delC frameshift_variant 0.14
fbiD 3339615 c.498G>T synonymous_variant 0.11
fbiD 3339734 p.Ala206Gly missense_variant 0.13
whiB7 3568425 c.255T>G synonymous_variant 0.25
fbiB 3641853 p.Gly107Cys missense_variant 0.15
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
rpoA 3878619 c.-113delC upstream_gene_variant 0.67
clpC1 4039686 p.Arg340His missense_variant 0.11
embC 4242111 p.Gly750Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4247028 p.Leu172Arg missense_variant 0.2
aftB 4268467 p.Val124Ile missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407560 p.Ser215Ala missense_variant 0.15
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0
Rv3236c 3612912 c.-454_204del conservative_inframe_deletion 1.0