TB-Profiler result

Run: ERR2245338

Summary

Run ID: ERR2245338

Sample name:

Date: 31-03-2023 17:38:59

Number of reads: 1311006

Percentage reads mapped: 99.02

Strain: lineage3.1.1

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 0.99
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
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 5710 c.471C>A synonymous_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7719 p.Glu140Lys missense_variant 0.25
gyrA 8414 c.1113C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575966 p.Val207Phe missense_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.22
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761476 p.Arg557His missense_variant 0.17
rpoB 762396 p.Arg864Cys missense_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764383 c.1014C>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779261 p.Thr91Asn missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303829 p.His300Leu missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102318 p.Glu242Gly missense_variant 0.12
katG 2154271 p.Ala614Glu missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Gly missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.27
PPE35 2170053 p.Thr187Ser missense_variant 0.29
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289233 c.9G>A synonymous_variant 0.15
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2519231 p.Tyr373His missense_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726439 p.Leu83Met missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474900 c.894C>T synonymous_variant 0.15
alr 3840557 c.864T>C synonymous_variant 0.12
alr 3841014 p.Arg136His missense_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.19
rpoA 3877498 p.Asp337Val missense_variant 0.13
rpoA 3878490 c.18C>G synonymous_variant 0.55
clpC1 4039031 c.1674T>C synonymous_variant 0.13
embC 4240016 p.Val52Ile missense_variant 0.17
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241013 p.Met384Arg missense_variant 0.21
embC 4241461 c.1599C>T synonymous_variant 0.21
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242720 p.Ala953Glu missense_variant 0.29
embA 4245113 c.1881C>A synonymous_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.23
embB 4246555 c.42G>C synonymous_variant 0.14
embB 4246556 p.Ala15Pro missense_variant 0.14
embB 4247025 p.Pro171Gln missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0