TB-Profiler result

Run: SRR11972171
Summary

Run ID: SRR11972171

Sample name:

Date: 03-04-2023 05:30:59

Number of reads: 509505

Percentage reads mapped: 97.29

Strain: lineage2.2.2

Drug-resistance: RR-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
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 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
rpoB 761166 p.Pro454Ser missense_variant 1.0 rifampicin
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 6490 c.-812T>A upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7546 p.Gly82Val missense_variant 0.13
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620537 p.Val216Gly missense_variant 0.29
rpoB 759615 c.-192A>C upstream_gene_variant 0.21
rpoB 759620 c.-187A>C upstream_gene_variant 0.25
rpoB 762399 p.Val865Met missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765890 p.Arg841Cys missense_variant 0.29
rpoC 767067 p.Leu1233Gln missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777191 c.1290C>A synonymous_variant 0.15
mmpL5 777196 p.Glu429Gln missense_variant 0.15
mmpL5 777226 p.Asn419Asp missense_variant 0.15
mmpL5 777227 c.1254C>T synonymous_variant 0.15
mmpL5 777612 p.Gly290Val missense_variant 0.2
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781832 c.273T>C synonymous_variant 0.12
fbiC 1302954 c.25delT frameshift_variant 0.13
fbiC 1303691 p.Pro254Gln missense_variant 0.18
Rv1258c 1406087 c.1254T>A synonymous_variant 0.18
Rv1258c 1406145 p.Ala399Val missense_variant 1.0
atpE 1461163 p.Ala40Asp missense_variant 0.14
atpE 1461192 p.Phe50Leu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.12
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.13
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.13
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.14
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.11
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.13
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.14
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.14
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.14
rrl 1474711 n.1054G>A non_coding_transcript_exon_variant 0.13
rrl 1475023 n.1366G>A non_coding_transcript_exon_variant 0.15
fabG1 1673324 c.-116G>T upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.42
rpsA 1834174 c.633C>T synonymous_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101663 c.1380G>A synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.14
PPE35 2167868 c.2745A>C synonymous_variant 0.21
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168140 p.Ala825Thr missense_variant 0.15
PPE35 2168143 p.Phe824Leu missense_variant 0.15
PPE35 2168150 c.2463T>C synonymous_variant 0.12
PPE35 2169269 c.1344A>G synonymous_variant 0.13
PPE35 2169272 c.1341C>G synonymous_variant 0.14
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.15
PPE35 2169988 p.Leu209Met missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.32
PPE35 2170053 p.Thr187Ser missense_variant 0.31
PPE35 2170406 c.207A>G synonymous_variant 0.12
Rv1979c 2222037 c.1128C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289986 c.-745T>A upstream_gene_variant 0.33
kasA 2518489 p.Ser125Arg missense_variant 0.18
kasA 2518809 p.Lys232Arg missense_variant 0.2
ahpC 2726557 p.Ala122Val missense_variant 0.17
Rv2752c 3067059 c.-868G>A upstream_gene_variant 0.17
thyA 3074648 c.-177T>G upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474568 p.Pro188Thr missense_variant 0.33
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840207 p.Ala405Asp missense_variant 0.18
alr 3840423 p.Arg333Lys missense_variant 0.33
rpoA 3877809 c.699G>A synonymous_variant 0.14
rpoA 3877951 p.Arg186His missense_variant 0.18
clpC1 4039161 p.His515Gly missense_variant 0.13
clpC1 4039169 p.Glu512Asp missense_variant 0.14
clpC1 4040057 c.648C>T synonymous_variant 0.22
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245482 c.2250G>A synonymous_variant 0.29
embB 4248196 p.Lys561Asn missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268797 p.Ala14Ser missense_variant 0.12
ethA 4326136 c.1338G>T synonymous_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338683 c.-162G>A upstream_gene_variant 0.15
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0