TB-Profiler result

Run: SRR21685256
Summary

Run ID: SRR21685256

Sample name:

Date: 04-04-2023 02:53:44

Number of reads: 499193

Percentage reads mapped: 99.55

Strain: lineage4.8

Drug-resistance: Other

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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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
gid 4407713 c.489delA frameshift_variant 0.11 streptomycin
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
ccsA 620475 c.585G>A synonymous_variant 1.0
ccsA 620540 p.Arg217Gln missense_variant 0.13
rpoB 762624 p.Val940Leu missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776991 p.Ile497Thr missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781920 p.Lys121* stop_gained 0.12
atpE 1460907 c.-138T>C upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476629 n.2972C>T non_coding_transcript_exon_variant 0.15
fabG1 1673357 c.-83G>A upstream_gene_variant 0.19
fabG1 1673359 c.-81T>C upstream_gene_variant 0.19
fabG1 1673361 c.-79C>G upstream_gene_variant 0.19
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
fabG1 1673679 c.242delC frameshift_variant 0.12
inhA 1674475 p.Val92Met missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918745 c.806A>G stop_lost&splice_region_variant 1.0
katG 2154564 p.Lys516Asn missense_variant 0.12
katG 2154614 p.Gln500Glu missense_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.13
PPE35 2167967 c.2646A>C synonymous_variant 0.14
PPE35 2169902 p.Leu237Phe missense_variant 0.15
PPE35 2169910 p.Asn235Tyr missense_variant 0.14
Rv1979c 2222952 p.Tyr71* stop_gained 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289479 c.-238G>C upstream_gene_variant 0.22
kasA 2518408 c.294C>A synonymous_variant 0.2
ahpC 2726341 p.Val50Gly missense_variant 0.29
folC 2747612 c.-14T>G upstream_gene_variant 1.0
thyX 3067358 c.588C>T synonymous_variant 0.12
thyA 3074395 p.Thr26Asn missense_variant 0.11
thyA 3074648 c.-177T>G upstream_gene_variant 0.35
ald 3087095 c.276C>T synonymous_variant 1.0
ald 3087255 p.Ala146Thr missense_variant 0.17
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fbiB 3641250 c.-285A>G upstream_gene_variant 0.12
fbiB 3641262 c.-273C>T upstream_gene_variant 0.13
clpC1 4038878 p.Gln609His missense_variant 0.14
clpC1 4040165 c.540G>A synonymous_variant 0.18
clpC1 4040453 c.252C>T synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245899 c.-615C>T upstream_gene_variant 1.0
embB 4246157 c.-357A>G upstream_gene_variant 0.27
embB 4247017 c.504G>T synonymous_variant 0.12
ethA 4326854 p.Arg207Leu missense_variant 0.11
ethR 4327980 p.Lys144Asn missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0