TB-Profiler result

Run: SRR4035559
Summary

Run ID: SRR4035559

Sample name:

Date: 04-04-2023 07:10:40

Number of reads: 817355

Percentage reads mapped: 99.52

Strain: lineage3

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
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
rpoB 761109 p.Asp435Tyr 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7381 p.Ser27Asn missense_variant 0.22
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8056 p.Arg252Leu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575203 c.-145C>G upstream_gene_variant 0.13
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760670 c.865delC frameshift_variant 0.2
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781750 p.Thr64Met missense_variant 0.17
rpsL 781896 p.Ala113Thr missense_variant 0.17
fbiC 1303016 p.Val29Gly missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102875 c.168C>T synonymous_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168751 c.1861delA frameshift_variant 0.22
PPE35 2169320 p.Leu431Phe missense_variant 0.33
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 2518237 c.123C>T synonymous_variant 0.18
eis 2715448 c.-116A>T upstream_gene_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726733 p.Gly181Ser missense_variant 0.22
folC 2746768 c.831G>A synonymous_variant 0.14
ribD 2987022 p.Met62Leu missense_variant 0.14
thyA 3073806 c.666C>G synonymous_variant 0.23
thyA 3074424 c.48G>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474073 c.67C>T synonymous_variant 0.13
Rv3236c 3613292 c.-177delG upstream_gene_variant 0.15
fbiA 3640639 p.Ala33Thr missense_variant 0.22
fbiB 3641955 p.Gly141Arg missense_variant 0.17
panD 4044110 p.Tyr58His missense_variant 0.12
embC 4239842 c.-21C>A upstream_gene_variant 0.3
embC 4240814 p.Gly318Cys missense_variant 0.11
embC 4241600 p.Met580Val missense_variant 0.12
embC 4242029 c.2167C>T synonymous_variant 0.15
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242986 p.Ala1042Thr missense_variant 0.12
embB 4246688 p.Pro59Ser missense_variant 0.13
embB 4247026 c.513G>A synonymous_variant 0.14
ethA 4328212 c.-740delC upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0