TB-Profiler result

Run: ERR1949966

Summary

Run ID: ERR1949966

Sample name:

Date: 31-03-2023 15:35:57

Number of reads: 835993

Percentage reads mapped: 83.31

Strain: lineage4

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
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
gyrB 7209 p.Asp657Ala missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7906 p.Phe202Ser missense_variant 0.11
gyrA 9506 c.2205C>T synonymous_variant 0.25
fgd1 491315 p.Gly178Ala missense_variant 0.29
mshA 576108 p.Ala254Gly missense_variant 0.17
mshA 576118 c.771C>T synonymous_variant 0.22
ccsA 619828 c.-63G>T upstream_gene_variant 0.17
rpoB 762240 p.Glu812* stop_gained 0.19
rpoB 763093 p.Val1096Ala missense_variant 0.12
rpoC 766865 p.Thr1166Pro missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775737 p.Leu915Pro missense_variant 0.13
mmpL5 775823 c.2658G>T synonymous_variant 0.2
mmpL5 776241 p.Lys747Thr missense_variant 0.14
mmpL5 777028 p.Thr485Ala missense_variant 0.17
mmpL5 777069 p.Ala471Gly missense_variant 0.14
mmpL5 777485 c.996T>C synonymous_variant 0.14
mmpL5 777663 p.Ala273Val missense_variant 0.15
mmpL5 778206 p.Met92Thr missense_variant 0.11
mmpS5 778597 p.Ile103Met missense_variant 0.12
mmpL5 778726 c.-246T>A upstream_gene_variant 0.27
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303153 p.Arg75Trp missense_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304560 p.Val544Leu missense_variant 0.25
fbiC 1304751 c.1821C>A synonymous_variant 0.14
Rv1258c 1406610 p.Ser244Ile missense_variant 0.18
Rv1258c 1406962 p.Met127Val missense_variant 0.18
Rv1258c 1407097 p.Ser82Ala missense_variant 0.38
embR 1417365 c.-18A>G upstream_gene_variant 0.12
atpE 1460882 c.-163T>A upstream_gene_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471740 n.-106A>T upstream_gene_variant 0.33
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.23
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.23
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.2
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.23
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474333 n.676A>G non_coding_transcript_exon_variant 0.12
rrl 1474943 n.1286A>G non_coding_transcript_exon_variant 0.22
rrl 1475002 n.1345A>T non_coding_transcript_exon_variant 0.25
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.2
inhA 1674244 p.Ile15Val missense_variant 0.12
tlyA 1917756 c.-184A>G upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918651 p.Glu238Gln missense_variant 0.12
ndh 2101709 p.Leu445Pro missense_variant 0.13
ndh 2102836 c.207T>C synonymous_variant 0.12
ndh 2102936 p.Ala36Asp missense_variant 0.25
ndh 2103064 c.-22A>C upstream_gene_variant 0.2
katG 2154622 p.Ile497Thr missense_variant 0.12
katG 2154671 p.Ser481Ala missense_variant 0.21
katG 2154769 p.Asp448Ala missense_variant 0.32
katG 2156176 c.-65A>G upstream_gene_variant 0.17
PPE35 2167716 p.Leu966Ser missense_variant 0.17
PPE35 2167879 p.Ser912Arg missense_variant 0.18
PPE35 2168228 c.2385C>A synonymous_variant 0.25
PPE35 2168554 p.Ile687Phe missense_variant 0.38
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170029 p.Met195Arg missense_variant 0.12
PPE35 2170492 p.Ala41Thr missense_variant 0.18
Rv1979c 2223010 p.Val52Ala missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223295 c.-131A>G upstream_gene_variant 0.11
pncA 2289465 c.-224G>C upstream_gene_variant 0.18
pncA 2289540 c.-299A>G upstream_gene_variant 0.22
kasA 2519062 c.948T>G synonymous_variant 0.12
eis 2714976 p.His119Gln missense_variant 0.2
ahpC 2726130 c.-63A>G upstream_gene_variant 0.11
folC 2746391 p.Val403Glu missense_variant 0.33
folC 2746426 c.1172delT frameshift_variant 0.17
pepQ 2859719 p.Thr234Pro missense_variant 0.17
pepQ 2860378 p.Ile14Thr missense_variant 0.11
pepQ 2860594 c.-176C>A upstream_gene_variant 0.22
ribD 2986757 c.-82C>G upstream_gene_variant 0.17
Rv2752c 3064566 c.1626G>C synonymous_variant 0.17
thyA 3073982 p.Tyr164His missense_variant 0.22
thyA 3074103 c.369C>A synonymous_variant 0.14
ald 3087339 p.Ile174Val missense_variant 0.17
fbiD 3339711 c.594A>C synonymous_variant 0.19
Rv3083 3448307 c.-197T>G upstream_gene_variant 0.23
whiB7 3568637 p.Leu15Met missense_variant 0.17
fbiA 3640448 c.-95A>T upstream_gene_variant 0.5
fbiA 3641239 p.Leu233Val missense_variant 0.23
alr 3841510 c.-90A>C upstream_gene_variant 0.2
alr 3841514 c.-94A>G upstream_gene_variant 0.2
rpoA 3878329 p.Leu60Gln missense_variant 0.2
rpoA 3878551 c.-44C>A upstream_gene_variant 1.0
clpC1 4038870 p.Glu612Val missense_variant 1.0
clpC1 4040522 p.Ser61Arg missense_variant 0.15
clpC1 4040553 p.Ser51* stop_gained 0.18
clpC1 4040861 c.-157T>A upstream_gene_variant 0.27
panD 4044315 c.-34A>G upstream_gene_variant 0.11
embC 4240128 p.Gln89Leu missense_variant 0.2
embC 4242308 p.Thr816Ser missense_variant 0.33
embC 4242482 p.Asn874Asp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242644 p.Asn928His missense_variant 0.15
embC 4242780 p.Asn973Ser missense_variant 0.11
embA 4244508 p.Leu426Val missense_variant 0.21
embA 4244761 p.Asn510Ile missense_variant 0.17
embA 4244861 c.1629G>A synonymous_variant 0.22
embA 4245250 p.His673Arg missense_variant 0.29
embB 4247901 p.Leu463Arg missense_variant 0.17
embB 4248254 p.Thr581Ala missense_variant 0.11
embB 4249431 p.Ser973* stop_gained 0.1
aftB 4267010 p.Glu609Asp missense_variant 0.18
aftB 4267641 p.Ala399Val missense_variant 0.25
aftB 4268478 p.Ala120Asp missense_variant 0.14
aftB 4268506 p.Arg111Gly missense_variant 0.14
aftB 4268619 p.Val73Gly missense_variant 0.2
ubiA 4269871 c.-38G>C upstream_gene_variant 0.25
ethA 4326163 c.1311T>C synonymous_variant 0.11
whiB6 4338261 c.261G>C synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448499 c.-4_*1408del transcript_ablation 1.0