TB-Profiler result

Run: ERR2229292
Summary

Run ID: ERR2229292

Sample name:

Date: 31-03-2023 16:57:54

Number of reads: 1004214

Percentage reads mapped: 98.97

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 575570 p.Ser75Gly missense_variant 0.11
mshA 576108 p.Ala254Gly missense_variant 0.4
mshA 576117 p.Ala257Gly missense_variant 0.2
ccsA 620656 p.Gly256Cys missense_variant 0.13
rpoC 766504 c.3135G>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776080 p.Ala801Ser missense_variant 0.15
mmpL5 776081 c.2400G>A synonymous_variant 0.15
mmpL5 777235 p.Asn416His missense_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303798 p.Val290Leu missense_variant 0.2
fbiC 1304223 c.1293G>T synonymous_variant 0.15
Rv1258c 1407243 p.Leu33Gln missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.11
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.11
fabG1 1673346 c.-94C>G upstream_gene_variant 0.26
fabG1 1673349 c.-91G>C upstream_gene_variant 0.28
fabG1 1673380 c.-60C>G upstream_gene_variant 0.16
inhA 1674872 p.Gln224Leu missense_variant 0.14
rpsA 1833974 p.Arg145Cys missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918507 p.Gly190Arg missense_variant 0.13
ndh 2102034 p.Ile337Val missense_variant 0.13
ndh 2103081 c.-39A>T upstream_gene_variant 0.13
katG 2155613 p.Phe167Leu missense_variant 0.11
PPE35 2168047 p.Leu856Val missense_variant 0.13
PPE35 2168051 c.2562G>C synonymous_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168776 p.Pro613Thr missense_variant 0.12
PPE35 2169602 c.1011C>A synonymous_variant 0.2
PPE35 2169910 p.Asn235Tyr missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.28
PPE35 2170053 p.Thr187Ser missense_variant 0.28
PPE35 2170385 c.228G>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714318 p.Arg339Trp missense_variant 0.17
pepQ 2859525 c.894T>C synonymous_variant 0.17
ribD 2987418 p.Gly194Ser missense_variant 0.17
Rv3236c 3612733 c.384C>A synonymous_variant 0.17
clpC1 4039530 p.Asp392Ala missense_variant 0.14
clpC1 4039829 p.Leu292Ile missense_variant 0.16
panD 4044123 c.159T>A synonymous_variant 0.15
embC 4239795 c.-68C>A upstream_gene_variant 0.22
embC 4239836 c.-27C>T upstream_gene_variant 0.15
embC 4241656 c.1794G>T synonymous_variant 0.18
embC 4242062 p.Trp734Arg missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244659 p.Leu476Pro missense_variant 0.13
embA 4246278 p.Ala1016Ser missense_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4248908 p.Ala799Ser missense_variant 0.12
aftB 4268752 p.Asp29Tyr missense_variant 0.15
ubiA 4269605 p.Asp77Asn missense_variant 0.22
ethR 4327718 p.Ser57Leu missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0