TB-Profiler result

Run: SRR12708417
Summary

Run ID: SRR12708417

Sample name:

Date: 02-08-2023 14:57:58

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
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 490769 c.-14A>G upstream_gene_variant 0.11
fgd1 490932 p.His50Gln missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575240 c.-108G>T upstream_gene_variant 0.11
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762140 c.2334G>T synonymous_variant 0.22
rpoB 762264 p.Gly820Cys missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763053 p.Leu1083Met missense_variant 0.17
rpoB 763222 p.Ile1139Thr missense_variant 0.18
rpoC 763680 p.Ile104Asn missense_variant 0.29
rpoC 765122 p.Leu585Val missense_variant 0.14
rpoC 765146 p.Pro593Thr missense_variant 0.14
rpoC 766128 p.Ala920Asp missense_variant 0.11
rpoC 766500 p.Ala1044Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777534 p.Thr316Asn missense_variant 0.14
mmpR5 779315 p.Arg109Leu missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303165 p.Ser79Gly missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833749 p.Ile70Leu missense_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168200 p.Ala805Thr missense_variant 0.29
PPE35 2168745 p.Gly623Ala missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519221 c.1107G>T synonymous_variant 0.14
eis 2714526 c.805_806delAC frameshift_variant 1.0
ahpC 2726043 c.-150C>T upstream_gene_variant 0.12
folC 2747226 p.Arg125Trp missense_variant 0.11
Rv2752c 3065711 p.Gly161Ser missense_variant 1.0
thyA 3074143 p.Asp110Val missense_variant 0.15
thyA 3074610 c.-139G>A upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087116 c.297G>A synonymous_variant 0.25
Rv3083 3449640 c.1137A>G synonymous_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613026 p.Ser31Pro missense_variant 0.15
alr 3841047 p.Leu125Pro missense_variant 0.13
alr 3841130 c.291G>A synonymous_variant 0.11
rpoA 3877884 c.624G>A synonymous_variant 0.33
clpC1 4039368 p.Lys446Met missense_variant 0.14
embC 4241515 c.1655delT frameshift_variant 0.2
embC 4242035 p.Gln725Lys missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243425 p.Gly65Trp missense_variant 0.13
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248172 c.1659G>T synonymous_variant 0.17
embB 4248590 p.Ala693Thr missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267782 p.Val352Asp missense_variant 0.18
ethA 4326454 c.1020C>T synonymous_variant 0.25
ethA 4327617 c.-144G>A upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0