TB-Profiler result

Run: ERR2229504
Summary

Run ID: ERR2229504

Sample name:

Date: 31-03-2023 17:15:39

Number of reads: 1003480

Percentage reads mapped: 99.36

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 0.3
mshA 576354 p.Leu336Gln missense_variant 0.12
mshA 576453 p.Val369Gly missense_variant 0.2
rpoC 765113 p.Val582Met missense_variant 0.13
rpoC 766688 p.Val1107Met 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.12
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.1
fabG1 1673346 c.-94C>G upstream_gene_variant 0.15
fabG1 1673349 c.-91G>C upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.32
fabG1 1673908 p.Lys157Glu missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918034 p.Val32Gly missense_variant 0.22
tlyA 1918403 p.Leu155Gln missense_variant 0.13
ndh 2101679 p.Ser455* stop_gained 0.12
ndh 2102971 c.72C>T synonymous_variant 0.14
PPE35 2168011 p.Ser868Gly missense_variant 0.2
PPE35 2168215 p.Thr800Ser missense_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.19
PPE35 2169272 c.1341C>G synonymous_variant 0.17
PPE35 2169278 c.1335T>C synonymous_variant 0.16
PPE35 2169281 c.1332T>G synonymous_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.47
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859775 p.Gly215Asp missense_variant 0.12
Rv2752c 3064563 c.1629A>G synonymous_variant 0.11
thyA 3074576 c.-105C>T upstream_gene_variant 0.12
fbiD 3339409 p.Ala98Ser missense_variant 0.17
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474053 p.Phe16Tyr missense_variant 0.18
whiB7 3568431 c.249C>G synonymous_variant 0.22
Rv3236c 3612478 c.639T>A synonymous_variant 0.2
Rv3236c 3612931 c.186G>T synonymous_variant 0.13
fbiA 3640673 p.Val44Ala missense_variant 0.11
fbiB 3641190 c.-345G>A upstream_gene_variant 0.13
fbiA 3641224 p.Gly228Trp missense_variant 0.14
fbiB 3642145 p.Leu204Ser missense_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242699 p.Val946Ala missense_variant 0.11
embC 4242750 p.Pro963Leu missense_variant 0.14
embA 4245684 p.Pro818Thr missense_variant 0.13
embA 4246240 p.Pro1003Gln missense_variant 0.13
embA 4246429 p.Ala1066Gly missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 1.0
embB 4246555 c.42G>C synonymous_variant 0.75
embB 4246556 p.Ala15Pro missense_variant 0.75
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.5
embB 4246584 p.Arg24Pro missense_variant 0.25
aftB 4268044 p.Ala265Pro missense_variant 0.11
ethA 4326941 p.Ile178Asn missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448498 c.-5_*1408del transcript_ablation 1.0