TB-Profiler result

Run: ERR2229609
Summary

Run ID: ERR2229609

Sample name:

Date: 31-03-2023 17:21:25

Number of reads: 915616

Percentage reads mapped: 99.25

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 6559 c.-743C>G upstream_gene_variant 0.11
gyrA 6595 c.-707G>A upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8874 p.Tyr525His missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.22
mshA 576766 c.1419G>C synonymous_variant 0.13
mshA 576772 c.1425T>A synonymous_variant 0.13
rpoB 760790 c.984C>T synonymous_variant 0.13
rpoC 764767 c.1398G>T synonymous_variant 0.12
rpoC 766833 p.Glu1155Val missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776755 p.Asp576Asn missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303510 p.Gly194Arg missense_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406410 c.931C>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rpsA 1833611 p.Ala24Ser missense_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918024 p.Ala29Pro missense_variant 0.12
ndh 2102539 c.504C>A synonymous_variant 0.12
katG 2155114 p.Leu333Pro missense_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169022 p.Gly531Arg missense_variant 0.14
PPE35 2169287 c.1326T>C synonymous_variant 0.13
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.64
PPE35 2170053 p.Thr187Ser missense_variant 0.62
PPE35 2170392 p.Gly74Ala missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289640 c.-399C>A upstream_gene_variant 0.14
eis 2714737 p.Glu199Gly missense_variant 0.11
folC 2746959 p.Gly214Trp missense_variant 0.12
ribD 2987026 p.Ala63Val missense_variant 0.12
thyX 3067206 p.Ala247Gly missense_variant 0.14
fbiB 3641568 p.Ile12Phe missense_variant 0.14
fbiB 3641941 p.Leu136Pro missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.23
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
clpC1 4038561 p.Asp715Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244184 p.Ser318Leu missense_variant 0.12
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4246563 p.Leu17Trp missense_variant 0.22
embB 4246567 c.54G>T synonymous_variant 0.22
embB 4247028 p.Leu172Arg missense_variant 0.21
embB 4249759 c.3246C>T synonymous_variant 0.17
aftB 4268624 c.213C>G synonymous_variant 0.25
ubiA 4269040 p.Asp265Gly missense_variant 0.11
ubiA 4269149 p.Val229Met missense_variant 0.33
ubiA 4269347 p.Ala163Thr missense_variant 0.12
ethR 4327909 p.Thr121Ala missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0