TB-Profiler result

Run: SRR18213686
Summary

Run ID: SRR18213686

Sample name:

Date: 03-04-2023 19:25:14

Number of reads: 492423

Percentage reads mapped: 85.93

Strain: lineage3

Drug-resistance: HR-TB

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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
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
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, 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 6391 c.-911G>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.38
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.21
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760933 p.Gly376Val missense_variant 0.33
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762545 c.-825C>A upstream_gene_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765964 p.Leu865Phe missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777106 p.Ser459Pro missense_variant 0.17
mmpL5 777110 c.1371T>A synonymous_variant 0.17
mmpL5 777119 p.His454Gln missense_variant 0.15
mmpL5 777122 c.1359C>T synonymous_variant 0.17
mmpL5 777128 c.1353A>G synonymous_variant 0.17
mmpL5 777136 p.Met449Leu missense_variant 0.13
mmpL5 777820 c.661C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800758 c.-51_-50insC upstream_gene_variant 0.11
fbiC 1302869 c.-62G>A upstream_gene_variant 0.11
fbiC 1303591 p.Arg221Trp missense_variant 0.17
fbiC 1303984 p.Asp352Asn missense_variant 0.11
fbiC 1304268 c.1338G>A synonymous_variant 0.17
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.11
Rv1258c 1406946 p.Ala132Gly missense_variant 0.11
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673598 p.Lys53Asn missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155880 c.232C>A synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168651 p.Leu654Phe 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 2518078 c.-37T>A upstream_gene_variant 0.11
eis 2714347 p.Phe329Tyr missense_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2860399 p.Arg7Gln missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841344 p.Thr26Lys missense_variant 0.1
alr 3841473 c.-53G>A upstream_gene_variant 1.0
alr 3841506 c.-86A>C upstream_gene_variant 0.2
ddn 3986748 c.-96G>A upstream_gene_variant 0.11
clpC1 4040472 p.Ile78Thr missense_variant 0.25
clpC1 4040568 p.Ala46Asp missense_variant 0.22
clpC1 4040781 c.-77G>T upstream_gene_variant 0.14
embC 4239973 c.111T>G synonymous_variant 0.21
embC 4241384 p.Pro508Ser missense_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243410 p.Ala60Pro missense_variant 0.11
embA 4243821 p.Thr197Ala missense_variant 0.12
aftB 4268297 c.540A>G synonymous_variant 0.12
aftB 4268561 c.276G>C synonymous_variant 0.25
whiB6 4338353 p.Pro57Thr missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0