TB-Profiler result

Run: SRR14088354
Summary

Run ID: SRR14088354

Sample name:

Date: 03-04-2023 09:45:20

Number of reads: 875255

Percentage reads mapped: 99.55

Strain: lineage3

Drug-resistance: Sensitive

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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
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 6416 p.Thr393Ser missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8613 p.Met438Val missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.23
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759750 c.-57G>A upstream_gene_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762484 p.Leu893Arg missense_variant 1.0
rpoB 762555 p.Pro917Ser missense_variant 0.1
rpoC 762956 c.-414G>T upstream_gene_variant 0.12
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
mmpL5 776533 p.Ala650Ser missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460868 c.-177A>G upstream_gene_variant 0.13
atpE 1461130 p.Gly29Asp missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471718 n.-128G>T upstream_gene_variant 0.2
rrl 1473449 n.-209G>A upstream_gene_variant 0.1
rrl 1473639 n.-19T>C upstream_gene_variant 0.18
fabG1 1673350 c.-90T>A upstream_gene_variant 0.18
fabG1 1673734 p.Arg99Gly missense_variant 0.12
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
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726520 p.Met110Leu missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473876 c.-131G>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474199 p.Lys65* stop_gained 0.11
Rv3236c 3612282 p.Gly279Ser missense_variant 0.11
Rv3236c 3612557 c.559delG frameshift_variant 0.12
Rv3236c 3613100 c.15_16delGG frameshift_variant 0.17
fbiB 3641901 p.Val123Phe missense_variant 0.11
rpoA 3877699 p.His270Arg missense_variant 0.1
clpC1 4039691 c.1014G>C synonymous_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248505 c.1992C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0