TB-Profiler result

Run: SRR13068983
Summary

Run ID: SRR13068983

Sample name:

Date: 03-04-2023 08:12:14

Number of reads: 157558

Percentage reads mapped: 99.27

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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
pncA 2288853 p.Val130Gly missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
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 7904 c.605delT frameshift_variant 0.67
fgd1 491163 p.Glu127Asp missense_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576388 c.1041G>C synonymous_variant 0.4
rpoC 766645 p.Glu1092Asp 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 777048 p.Ile478Thr missense_variant 0.29
mmpL5 777237 p.Tyr415Cys missense_variant 0.17
mmpR5 779206 p.Met73Leu missense_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303486 p.Gly186Arg missense_variant 0.22
fbiC 1304093 p.Met388Thr missense_variant 0.29
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rpsA 1833763 c.222C>T synonymous_variant 0.25
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986998 p.Thr54Ala missense_variant 0.29
Rv2752c 3065713 p.Thr160Asn missense_variant 0.5
thyX 3068093 c.-148A>G upstream_gene_variant 0.4
thyA 3074425 p.Thr16Met missense_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 0.25
Rv3083 3448848 c.345T>C synonymous_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474913 p.Ala303Pro missense_variant 0.29
fprA 3475002 c.996G>A synonymous_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640731 c.-804C>T upstream_gene_variant 0.18
rpoA 3878111 c.396delC frameshift_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244372 c.1140T>C synonymous_variant 0.33
embB 4246762 c.249G>A synonymous_variant 0.4
embB 4247464 c.951C>T synonymous_variant 0.22
ubiA 4269271 p.Val188Ala missense_variant 1.0
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