TB-Profiler result

Run: ERR1949982
Summary

Run ID: ERR1949982

Sample name:

Date: 31-03-2023 15:36:30

Number of reads: 492254

Percentage reads mapped: 99.65

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
ethA 4327082 c.391delT frameshift_variant 0.13 ethionamide
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 5527 c.288C>G synonymous_variant 0.1
gyrB 6971 p.Pro578Thr missense_variant 0.23
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7826 c.525C>A synonymous_variant 0.25
gyrA 9274 p.Glu658Val missense_variant 0.29
fgd1 491018 p.Phe79Tyr missense_variant 0.15
fgd1 491061 p.Met93Ile missense_variant 0.22
fgd1 491792 c.1010G>A splice_region_variant&stop_retained_variant 0.25
mshA 575158 c.-190C>T upstream_gene_variant 0.17
mshA 575472 p.Asp42Ala missense_variant 0.17
ccsA 620152 p.Ile88Phe missense_variant 0.25
ccsA 620330 p.Ile147Thr missense_variant 0.11
rpoB 760839 p.Gly345Cys missense_variant 0.12
rpoC 764038 p.Trp223Cys missense_variant 0.17
rpoC 764541 p.Val391Gly missense_variant 0.17
rpoC 764543 p.Thr392Asp missense_variant 0.15
rpoC 764651 p.Ser428Ala missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776073 p.Val803Gly missense_variant 0.33
mmpL5 776443 p.Phe680Val missense_variant 0.29
mmpL5 776799 p.Val561Glu missense_variant 0.22
mmpL5 777897 p.Asp195Gly missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1407006 p.Leu112Arg missense_variant 0.25
embR 1417080 p.Pro90Thr missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rpsA 1833954 p.Leu138Pro missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168133 p.Asp827Ala missense_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169707 c.906T>A synonymous_variant 0.29
Rv1979c 2221941 c.1224G>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290190 c.-949C>A upstream_gene_variant 0.14
kasA 2519153 p.Ile347Val missense_variant 0.25
pepQ 2859345 c.1074C>A synonymous_variant 0.23
pepQ 2860246 p.Gly58Asp missense_variant 0.5
Rv2752c 3064566 c.1626G>C synonymous_variant 0.25
Rv2752c 3064756 p.Val479Gly missense_variant 0.5
fprA 3475007 p.Phe334Cys missense_variant 0.25
fbiA 3641494 p.Glu318Lys missense_variant 0.18
fbiB 3642148 p.Val205Gly missense_variant 0.25
alr 3840810 p.Asp204Gly missense_variant 0.11
alr 3841509 c.-89A>G upstream_gene_variant 0.29
clpC1 4038223 p.Ala828Thr missense_variant 0.18
clpC1 4038389 c.2315delC frameshift_variant 0.18
clpC1 4039483 p.Ala408Pro missense_variant 0.22
clpC1 4040027 c.678C>T synonymous_variant 0.15
clpC1 4040892 c.-188A>G upstream_gene_variant 0.14
embC 4240363 p.Glu167Asp missense_variant 0.14
embC 4240541 p.Thr227Pro missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243089 p.Asn1076Ile missense_variant 0.14
embA 4243912 p.Leu227Arg missense_variant 0.17
embB 4248364 c.1851G>T synonymous_variant 0.12
aftB 4267457 p.Trp460* stop_gained 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0