TB-Profiler result

Run: ERR2229121
Summary

Run ID: ERR2229121

Sample name:

Date: 31-03-2023 16:42:26

Number of reads: 875693

Percentage reads mapped: 99.46

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
fgd1 491502 p.Glu240Asp missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.42
rpoB 761869 p.Asp688Val missense_variant 0.12
rpoC 764026 p.Leu219Phe missense_variant 0.2
rpoC 764766 p.Ala466Glu missense_variant 0.12
rpoC 765006 c.1640delT frameshift_variant 0.15
rpoC 765459 p.Ile697Asn missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
atpE 1460913 c.-132G>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472207 n.362A>G non_coding_transcript_exon_variant 0.15
rrl 1473651 n.-7G>A upstream_gene_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.16
fabG1 1673349 c.-91G>C upstream_gene_variant 0.16
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.36
fabG1 1674009 p.Met190Ile missense_variant 0.12
rpsA 1834892 p.Ala451Thr missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102450 p.Lys198Arg missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168812 p.Thr601Ser missense_variant 0.12
PPE35 2169287 c.1326T>C synonymous_variant 0.16
PPE35 2169879 p.Phe245Ser missense_variant 0.11
PPE35 2169882 p.Ser244Asn missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289542 c.-302delG upstream_gene_variant 0.13
pncA 2289550 c.-310delC upstream_gene_variant 0.13
kasA 2518685 p.Asp191Asn missense_variant 0.17
kasA 2519140 c.1026G>C synonymous_variant 0.12
kasA 2519143 c.1029G>C synonymous_variant 0.13
eis 2714170 p.Ala388Glu missense_variant 0.15
eis 2715155 p.Gly60Arg missense_variant 0.12
ahpC 2726188 c.-5G>T upstream_gene_variant 0.12
ald 3087316 p.Val166Ala missense_variant 0.18
ald 3087319 c.500_501insTC frameshift_variant 0.18
ald 3087334 p.Val172Ala missense_variant 0.25
ald 3087337 c.519_520delGA frameshift_variant 0.22
ald 3087343 p.Gly175Asp missense_variant 0.22
fbiD 3339711 c.594A>T synonymous_variant 0.12
alr 3841612 c.-193_-192insC upstream_gene_variant 0.13
rpoA 3877656 c.852T>C synonymous_variant 0.14
rpoA 3877691 p.Gly273Ser missense_variant 0.12
embC 4240923 p.Thr354Asn missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244898 p.Thr556Ser missense_variant 0.22
embB 4246544 p.Thr11Pro missense_variant 0.36
embB 4246548 p.Pro12Gln missense_variant 0.38
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4246567 c.54G>T synonymous_variant 0.29
embB 4247028 p.Leu172Gln missense_variant 0.29
embB 4248617 p.Leu702Met missense_variant 0.13
embB 4249339 c.2826T>C synonymous_variant 0.14
ethA 4328434 c.-961C>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0