TB-Profiler result

Run: ERR2228828
Summary

Run ID: ERR2228828

Sample name:

Date: 31-03-2023 16:22:18

Number of reads: 923690

Percentage reads mapped: 99.28

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 0.99
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
gyrB 6720 p.Asp494Ala missense_variant 0.2 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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 6181 c.942C>A synonymous_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 0.95
fgd1 491016 c.234C>A synonymous_variant 0.29
fgd1 491315 p.Gly178Ala missense_variant 0.18
fgd1 491657 p.Glu292Gly missense_variant 0.2
mshA 575387 p.Ala14Pro missense_variant 0.11
ccsA 620671 p.Trp261Gly missense_variant 0.24
ccsA 620830 p.Thr314Pro missense_variant 0.13
rpoB 762254 c.2448T>G synonymous_variant 0.17
rpoB 762472 p.Ile889Ser missense_variant 0.29
rpoC 764462 p.Ile365Val missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779066 p.Tyr26Phe missense_variant 0.27
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406929 p.Ser138Ala missense_variant 0.32
embR 1416518 p.Leu277Arg missense_variant 0.19
embR 1416994 p.Glu118Asp missense_variant 0.25
atpE 1460948 c.-97A>T upstream_gene_variant 0.3
atpE 1461142 p.Asn33Ser missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472538 n.693A>T non_coding_transcript_exon_variant 0.2
rrl 1473976 n.319T>A non_coding_transcript_exon_variant 0.25
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475607 n.1950A>T non_coding_transcript_exon_variant 0.2
rrl 1476162 n.2505A>T non_coding_transcript_exon_variant 0.25
inhA 1674821 p.Leu207Arg missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155166 p.Gly316Cys missense_variant 0.22
katG 2155305 c.807T>G synonymous_variant 0.27
PPE35 2168728 p.Gly629Arg missense_variant 1.0
Rv1979c 2222163 c.1002G>A synonymous_variant 0.18
Rv1979c 2222775 c.390C>A synonymous_variant 0.33
Rv1979c 2223006 p.Leu53Phe missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289423 c.-182A>G upstream_gene_variant 0.22
pncA 2289866 c.-625T>G upstream_gene_variant 0.29
pncA 2290042 c.-801T>G upstream_gene_variant 0.33
eis 2714901 c.432A>C synonymous_variant 0.25
folC 2747036 p.Asn188Thr missense_variant 0.18
pepQ 2859678 c.741A>T synonymous_variant 0.38
ribD 2987290 p.Asp151Ala missense_variant 0.15
Rv2752c 3064566 c.1626G>C synonymous_variant 0.22
Rv2752c 3065677 p.Lys172Arg missense_variant 0.11
Rv2752c 3065779 p.Val138Glu missense_variant 0.2
thyX 3067390 p.Thr186Pro missense_variant 0.58
whiB7 3568465 p.Asp72Ala missense_variant 0.25
Rv3236c 3612039 p.Phe360Val missense_variant 0.15
Rv3236c 3612078 p.Ser347Ala missense_variant 0.27
Rv3236c 3612748 c.369G>T synonymous_variant 0.17
fbiB 3642280 p.Leu249Arg missense_variant 0.25
rpoA 3877891 p.Asp206Ala missense_variant 0.27
rpoA 3878490 c.18C>G synonymous_variant 0.29
clpC1 4038492 p.Val738Gly missense_variant 0.33
clpC1 4039594 p.Arg371Gly missense_variant 0.13
clpC1 4039730 c.975C>G synonymous_variant 0.11
embC 4242245 p.Thr795Pro missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 0.96
embA 4244854 p.Val541Gly missense_variant 0.67
embA 4244905 p.Val558Gly missense_variant 0.33
embA 4245381 p.Thr717Pro missense_variant 0.2
embA 4245397 p.Asn722Thr missense_variant 0.33
embA 4245402 p.Thr724Pro missense_variant 0.3
embA 4245688 p.Val819Gly missense_variant 0.33
embA 4245721 p.Phe830Cys missense_variant 0.29
embB 4246736 p.Thr75Pro missense_variant 0.38
aftB 4267564 p.Thr425Pro missense_variant 0.12
ubiA 4269059 p.Ile259Val missense_variant 0.14
ethA 4327077 p.Phe133Ile missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0