TB-Profiler result

Run: SRR4033201
Summary

Run ID: SRR4033201

Sample name:

Date: 04-04-2023 05:54:32

Number of reads: 2094328

Percentage reads mapped: 99.6

Strain: lineage2.2.1

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 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
rpoB 761139 p.His445Tyr 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
gyrB 5059 c.-181G>A upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8014 p.Gln238Arg missense_variant 0.15
gyrA 9264 p.Asp655Asn missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9323 c.2022C>T synonymous_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.96
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759664 c.-143G>A upstream_gene_variant 0.13
rpoB 759667 c.-140C>T upstream_gene_variant 0.14
rpoB 760154 c.348C>T synonymous_variant 0.12
rpoB 760313 c.507G>T synonymous_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765013 c.1644C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.95
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777275 c.1206C>T synonymous_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1461072 p.Leu10Ile missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476132 n.2475G>A non_coding_transcript_exon_variant 0.17
fabG1 1673549 p.Ala37Val missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101790 p.Thr418Met missense_variant 0.11
katG 2153970 p.Asp714Glu missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156105 p.Glu3Lys missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.19
PPE35 2169355 p.Gly420Cys missense_variant 0.12
PPE35 2169866 c.747G>C synonymous_variant 0.25
Rv1979c 2222120 c.1044delG frameshift_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2725954 c.-239C>T upstream_gene_variant 0.11
ahpC 2726604 c.413delT frameshift_variant 0.11
thyA 3073806 c.666C>G synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474039 c.33C>T synonymous_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642820 p.Ala429Val missense_variant 0.12
alr 3841258 p.His55Tyr missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.22
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246567 c.54G>T synonymous_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267948 p.Asp297Tyr missense_variant 0.18
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