TB-Profiler result

Run: SRR4035494
Summary

Run ID: SRR4035494

Sample name:

Date: 04-04-2023 07:07:41

Number of reads: 1533727

Percentage reads mapped: 99.43

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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8056 p.Arg252Leu missense_variant 1.0
gyrA 8949 p.Lys550Glu missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576287 p.Arg314Trp missense_variant 0.15
mshA 576460 c.1113C>T synonymous_variant 0.22
mshA 576485 p.Ala380Ser missense_variant 0.2
mshA 576494 p.Asp383Tyr missense_variant 0.22
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
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 776073 c.2407delG frameshift_variant 0.13
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777017 c.1464C>T synonymous_variant 0.12
mmpL5 777517 p.Phe322Leu missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305220 p.Arg764Ser missense_variant 0.13
fbiC 1305225 c.2295C>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473927 n.270C>G non_coding_transcript_exon_variant 0.11
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.13
fabG1 1673888 p.Gln150Arg missense_variant 0.12
inhA 1673898 c.-304C>T upstream_gene_variant 0.12
inhA 1674544 p.Asp115Asn missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918205 p.Ala89Val missense_variant 0.14
tlyA 1918396 p.Ala153Pro missense_variant 0.13
ndh 2102406 p.Leu213Val missense_variant 0.11
ndh 2102767 c.276C>T synonymous_variant 0.15
ndh 2102929 c.114T>C synonymous_variant 0.1
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
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.96
pncA 2290082 c.-841A>G upstream_gene_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyX 3067654 p.His98Asn missense_variant 0.15
thyA 3073806 c.666C>G synonymous_variant 0.14
thyA 3074424 c.48G>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339589 c.472C>T synonymous_variant 0.15
Rv3083 3449437 c.934_935insC frameshift_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474718 p.Ala238Pro missense_variant 0.12
fprA 3474736 p.Val244Leu missense_variant 0.12
Rv3236c 3613207 c.-91G>A upstream_gene_variant 0.12
clpC1 4038857 c.1848C>A synonymous_variant 0.25
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247219 c.706T>C synonymous_variant 0.14
embB 4247361 p.Val283Ala missense_variant 0.12
aftB 4267477 p.Ser454Pro missense_variant 0.11
aftB 4268032 p.Pro269Ala missense_variant 0.13
aftB 4268801 c.36G>C synonymous_variant 0.11
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