TB-Profiler result

Run: ERR4407542
Summary

Run ID: ERR4407542

Sample name:

Date: 01-04-2023 05:49:19

Number of reads: 336684

Percentage reads mapped: 99.65

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 7600 p.Ala100Asp missense_variant 0.2
gyrA 7811 c.510C>T synonymous_variant 0.11
mshA 576686 c.1340delA frameshift_variant 0.33
rpoB 761548 p.Val581Gly missense_variant 0.13
rpoB 762711 p.Pro969Ser missense_variant 0.14
rpoB 762869 p.Tyr1021* stop_gained 0.11
rpoC 764467 c.1098C>A synonymous_variant 0.14
rpoC 764752 c.1383G>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777829 p.Met218Leu missense_variant 0.18
mmpS5 778640 p.Ser89Leu missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801080 p.Ala91Val missense_variant 0.12
fbiC 1303161 c.231G>A synonymous_variant 0.2
fbiC 1303210 p.Val94Phe missense_variant 0.12
fbiC 1303272 c.342A>T synonymous_variant 0.15
fbiC 1304904 c.1974G>A synonymous_variant 0.18
Rv1258c 1406795 c.546G>A synonymous_variant 0.17
embR 1417091 p.Ala86Val missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473333 n.1488T>C non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475863 n.2206G>T non_coding_transcript_exon_variant 0.18
rrl 1476641 n.2984T>C non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155067 p.Gly349Cys missense_variant 0.12
katG 2155167 c.945C>T synonymous_variant 0.11
katG 2155332 c.780C>T synonymous_variant 0.33
katG 2156044 p.Val23Ala missense_variant 0.33
katG 2156367 c.-256G>A upstream_gene_variant 0.18
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169752 c.861C>T synonymous_variant 0.5
PPE35 2170162 p.Met151Leu missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518910 c.796C>T synonymous_variant 0.17
eis 2714415 c.918G>A synonymous_variant 0.13
folC 2746408 c.1191G>A synonymous_variant 0.25
pepQ 2859700 p.Gly240Asp missense_variant 0.14
pepQ 2859801 c.618G>A synonymous_variant 0.17
Rv2752c 3065572 p.Glu207Gly missense_variant 0.17
thyA 3074168 c.303delG frameshift_variant 0.12
ald 3086636 c.-184A>G upstream_gene_variant 0.12
ald 3086646 c.-174G>T upstream_gene_variant 0.13
fprA 3474063 c.57G>C synonymous_variant 0.11
fprA 3474138 c.132T>C synonymous_variant 0.12
fprA 3474780 c.774C>A synonymous_variant 0.12
fprA 3475367 p.Gly454Val missense_variant 0.4
fbiA 3641524 p.Gly328Arg missense_variant 0.25
rpoA 3878484 c.22_23dupAC frameshift_variant 0.22
clpC1 4038744 p.Thr654Met missense_variant 0.13
clpC1 4039123 p.Val528Leu missense_variant 0.14
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4040364 p.Arg114Gln missense_variant 0.1
embC 4239936 c.75dupC frameshift_variant 0.12
embA 4242304 c.-929G>C upstream_gene_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243347 p.Thr39Ala missense_variant 0.1
embA 4244539 p.Ala436Val missense_variant 0.13
embA 4244872 p.Gly547Val missense_variant 0.22
embA 4245325 p.Val698Ala missense_variant 0.17
embA 4245561 p.Val777Met missense_variant 0.12
aftB 4267430 c.1406delC frameshift_variant 0.14
aftB 4267782 p.Val352Gly missense_variant 1.0
ubiA 4269482 p.Trp118Arg missense_variant 0.14
aftB 4269684 c.-848G>A upstream_gene_variant 0.13
ethA 4328216 c.-743C>A upstream_gene_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0