TB-Profiler result

Run: ERR2229678
Summary

Run ID: ERR2229678

Sample name:

Date: 31-03-2023 17:24:44

Number of reads: 661881

Percentage reads mapped: 99.61

Strain: lineage4.8

Drug-resistance: HR-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
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
katG 2154014 p.Ser700Pro missense_variant 0.22 isoniazid
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
fgd1 491776 c.994T>C synonymous_variant 0.12
mshA 576441 p.Cys365Phe missense_variant 0.1
mshA 576771 p.Arg475Leu missense_variant 0.11
rpoB 759615 c.-192A>C upstream_gene_variant 0.17
rpoB 759954 p.Val50Ile missense_variant 0.11
rpoB 759972 p.Glu56Lys missense_variant 0.12
rpoB 761259 p.Gly485Trp missense_variant 0.17
rpoC 763526 p.Gly53Trp missense_variant 0.11
rpoC 763852 c.483C>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777396 p.Ser362Ile missense_variant 0.22
mmpL5 777478 p.Leu335Phe missense_variant 0.17
mmpR5 779158 p.Ala57Leu missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304109 c.1179C>T synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473737 n.80G>T non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673359 c.-81T>C upstream_gene_variant 0.1
fabG1 1673361 c.-79C>G upstream_gene_variant 0.1
fabG1 1673560 p.Lys41Leu missense_variant 0.15
rpsA 1834859 p.Ala440Pro missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101813 p.Lys410Asn missense_variant 0.18
ndh 2101981 c.1062C>A synonymous_variant 0.12
ndh 2103225 c.-183A>C upstream_gene_variant 0.31
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169991 p.Gly208Cys missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518375 c.261C>A synonymous_variant 0.12
kasA 2518683 p.Ala190Val missense_variant 0.15
kasA 2518686 p.Asp191Gly missense_variant 0.17
kasA 2519057 p.Thr315Ser missense_variant 0.15
kasA 2519061 p.Pro316Arg missense_variant 0.18
kasA 2519078 p.Glu322Leu missense_variant 0.29
kasA 2519083 c.970_976delAACGCCA frameshift_variant 0.33
kasA 2519097 p.Val328Gly missense_variant 0.33
pepQ 2859707 p.Val238Leu missense_variant 0.11
Rv2752c 3064534 p.Pro553Leu missense_variant 0.17
thyX 3067529 c.417C>A synonymous_variant 0.14
thyX 3067748 c.198C>T synonymous_variant 0.1
thyA 3074259 p.Trp71Cys missense_variant 0.1
ald 3086938 p.Gly40Val missense_variant 0.1
fbiD 3339078 c.-40C>A upstream_gene_variant 0.14
Rv3236c 3612060 p.Ala353Thr missense_variant 0.11
Rv3236c 3612504 p.His205Tyr missense_variant 0.11
fbiB 3641997 p.Ala155Ser missense_variant 0.25
alr 3840882 p.Arg180Leu missense_variant 0.17
rpoA 3878069 p.Val147Ile missense_variant 0.1
clpC1 4038752 p.Gln651His missense_variant 0.1
clpC1 4039321 p.Ala462Ser missense_variant 0.11
clpC1 4040144 c.561G>C synonymous_variant 0.13
clpC1 4040172 p.Leu178His missense_variant 0.2
embC 4240648 c.786C>T synonymous_variant 0.25
embC 4241034 p.Pro391Gln missense_variant 0.22
embC 4241538 p.Gly559Asp missense_variant 1.0
embC 4241549 p.Gly563* stop_gained 0.14
embC 4241658 p.Ser599* stop_gained 0.2
embC 4242230 p.Ile790Leu missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267233 p.Asp535Val missense_variant 0.11
whiB6 4338395 p.Thr43Ala missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0