TB-Profiler result

Run: ERR11068499

Summary

Run ID: ERR11068499

Sample name:

Date: 06-04-2023 15:03:08

Number of reads: 3609141

Percentage reads mapped: 99.35

Strain: lineage3.1.2

Drug-resistance: Other


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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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 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
ethA 4326858 p.Gln206* stop_gained 0.12 ethionamide
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 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490682 c.-101C>T upstream_gene_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575198 c.-150C>T upstream_gene_variant 0.15
mshA 575447 p.Ser34Pro missense_variant 0.14
mshA 575926 c.582dupC frameshift_variant 0.5
ccsA 619889 c.-2G>T upstream_gene_variant 0.14
ccsA 620292 c.402C>T synonymous_variant 0.1
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764327 p.Ile320Phe missense_variant 0.17
rpoC 764552 p.Gly395Cys missense_variant 0.14
rpoC 766082 p.Ala905Thr missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801241 p.His145Tyr missense_variant 0.22
rplC 801279 c.471G>A synonymous_variant 0.11
fbiC 1303178 p.Ala83Val missense_variant 1.0
fbiC 1305455 p.Arg842His missense_variant 0.25
Rv1258c 1406137 p.Glu402Lys missense_variant 0.12
Rv1258c 1407509 c.-169C>T upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833389 c.-153G>T upstream_gene_variant 1.0
rpsA 1834956 p.Ala472Val missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101666 c.1377T>C synonymous_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155782 c.330C>A synonymous_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518998 p.Leu295Pro missense_variant 0.2
eis 2714755 p.Pro193Gln missense_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 0.99
ribD 2987342 c.504C>T synonymous_variant 0.33
Rv2752c 3065383 p.Met270Arg missense_variant 0.56
Rv2752c 3067180 c.-989C>T upstream_gene_variant 0.12
thyX 3067211 c.735G>A synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339323 p.Ala69Val missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641595 p.Pro21Ser missense_variant 0.18
fbiB 3642024 p.Ala164Thr missense_variant 0.18
fbiB 3642039 p.Gly169Ser missense_variant 0.17
panD 4044476 c.-195G>A upstream_gene_variant 0.2
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242314 p.Ser818Arg missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244205 p.Arg325Cys missense_variant 0.13
embA 4245450 c.2218C>T synonymous_variant 0.11
embB 4246792 c.279C>T synonymous_variant 0.17
embB 4247852 p.Thr447Pro missense_variant 0.17
embB 4248409 p.Leu632Phe missense_variant 0.2
ubiA 4270029 c.-196G>T upstream_gene_variant 0.17
ethR 4328047 p.Pro167Ser missense_variant 0.25
ethA 4328471 c.-998A>G upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0