TB-Profiler result

Run: ERR2245281
Summary

Run ID: ERR2245281

Sample name:

Date: 31-03-2023 17:37:00

Number of reads: 2185477

Percentage reads mapped: 99.27

Strain: lineage3.1.1

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
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
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 5369 p.His44Asn missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8667 p.Ala456Ser missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>A synonymous_variant 0.13
fgd1 491315 p.Gly178Ala missense_variant 0.29
fgd1 491342 p.Arg187Leu missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.4
ccsA 620455 p.Ala189Thr missense_variant 0.17
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762802 p.Asp999Val missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766235 p.Gly956Arg missense_variant 0.11
rpoC 766369 c.3000C>A synonymous_variant 0.18
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
fbiC 1303284 c.354T>C synonymous_variant 0.12
fbiC 1304365 p.Gln479Glu missense_variant 0.13
fbiC 1304870 p.Leu647Gln missense_variant 0.13
Rv1258c 1406957 c.384G>T synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673612 p.Val58Gly missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155944 p.Asp56Glu missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168428 c.2184delG frameshift_variant 0.14
PPE35 2168876 p.Phe579Leu missense_variant 0.2
PPE35 2169053 c.1560T>A synonymous_variant 0.2
PPE35 2169063 p.Met517Lys missense_variant 0.25
PPE35 2169893 c.720C>A synonymous_variant 0.14
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2169910 p.Asn235Tyr missense_variant 0.22
PPE35 2170461 p.Gly51Glu missense_variant 1.0
PPE35 2170551 p.Ser21Cys missense_variant 0.15
Rv1979c 2223190 c.-26A>G upstream_gene_variant 0.13
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
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746319 p.Pro427His missense_variant 0.22
folC 2746773 p.Val276Leu missense_variant 0.25
Rv2752c 3065424 c.768C>T synonymous_variant 0.15
thyA 3074066 p.Gly136Ser missense_variant 0.13
thyA 3074130 c.342G>T synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448889 p.Arg129Leu missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474165 c.159C>G synonymous_variant 0.11
fprA 3474967 p.Ser321Ala missense_variant 0.25
fprA 3475083 p.Trp359Cys missense_variant 0.18
Rv3236c 3612432 p.Val229Leu missense_variant 0.18
Rv3236c 3612828 p.Ile97Phe missense_variant 0.2
Rv3236c 3613295 c.-179G>T upstream_gene_variant 0.13
fbiB 3641616 p.Asp28Asn missense_variant 0.18
fbiB 3641669 c.135C>A synonymous_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.21
rpoA 3878490 c.18C>G synonymous_variant 0.33
ddn 3986852 c.9A>G synonymous_variant 0.12
clpC1 4039031 c.1674T>C synonymous_variant 0.17
clpC1 4039508 c.1197G>C synonymous_variant 0.15
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242450 p.Met863Arg missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242850 c.-383G>T upstream_gene_variant 0.18
embA 4243334 c.102T>C synonymous_variant 0.12
embA 4244155 p.Thr308Arg missense_variant 0.1
embA 4245286 p.Leu685Ser missense_variant 0.12
embB 4246598 p.Val29Met missense_variant 0.12
embB 4247028 p.Leu172Gln missense_variant 0.2
embB 4247740 c.1227G>T synonymous_variant 0.17
embB 4248861 p.Val783Gly missense_variant 0.17
aftB 4267805 c.1032T>C synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0