TB-Profiler result

Run: ERR2229819
Summary

Run ID: ERR2229819

Sample name:

Date: 31-03-2023 17:36:48

Number of reads: 506964

Percentage reads mapped: 99.58

Strain: lineage4

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
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 2155167 p.Ser315Arg missense_variant 0.13 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
gyrB 5722 c.483G>A synonymous_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7448 p.Lys49Asn missense_variant 0.15
fgd1 490693 c.-90G>A upstream_gene_variant 0.14
mshA 575323 c.-25G>T upstream_gene_variant 0.18
mshA 575903 p.Ala186Thr missense_variant 0.22
mshA 575977 c.630G>T synonymous_variant 0.14
mshA 576089 c.750_769delTGATCGGCGCGCGGCCCGGG frameshift_variant 0.15
ccsA 620051 p.Val54Glu missense_variant 0.22
rpoB 759620 c.-187A>C upstream_gene_variant 0.27
rpoB 762387 p.Glu861Lys missense_variant 0.17
rpoC 765564 p.Ser732Leu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775891 p.Ala864Thr missense_variant 0.13
mmpL5 777658 p.Thr275Ser missense_variant 0.4
mmpS5 778778 p.Val43Asp missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781597 p.Arg13Leu missense_variant 0.15
rplC 800725 c.-84C>T upstream_gene_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304961 c.2031C>A synonymous_variant 0.13
atpE 1461181 p.Gln46Arg missense_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 1474974 n.1317G>T non_coding_transcript_exon_variant 0.15
fabG1 1673798 p.Ala120Asp missense_variant 0.2
inhA 1674525 p.Phe108Leu missense_variant 0.11
inhA 1674930 c.729C>T synonymous_variant 0.22
rpsA 1834831 c.1290G>C synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918178 p.Ala80Val missense_variant 0.11
ndh 2101976 p.Pro356Gln missense_variant 0.13
ndh 2102309 p.Leu245Pro missense_variant 0.12
ndh 2103062 c.-20C>A upstream_gene_variant 0.13
katG 2154270 c.1842G>A synonymous_variant 0.2
katG 2156267 c.-156A>G upstream_gene_variant 0.12
PPE35 2168187 p.Phe809Ser missense_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168872 c.1741C>T synonymous_variant 0.18
PPE35 2169398 c.1215C>A synonymous_variant 0.15
PPE35 2169943 p.Leu224Ile missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288793 p.Gly150Val missense_variant 0.11
pncA 2288891 c.351G>T synonymous_variant 0.17
pepQ 2860127 p.Glu98Lys missense_variant 0.17
ribD 2986855 p.Gln6Arg missense_variant 0.1
Rv2752c 3064770 c.1422G>T synonymous_variant 0.17
Rv2752c 3065902 p.Arg97Leu missense_variant 0.2
Rv2752c 3067113 c.-922C>A upstream_gene_variant 0.33
thyA 3073869 p.Trp201* stop_gained 0.13
ald 3087694 p.Asp292Gly missense_variant 0.15
fprA 3474600 c.594G>T synonymous_variant 0.11
fbiB 3640965 c.-570C>G upstream_gene_variant 0.33
fbiB 3641702 p.Cys56* stop_gained 0.12
fbiB 3642528 p.Glu332* stop_gained 0.2
alr 3841132 p.Ala97Ser missense_variant 0.12
ddn 3986822 c.-22C>A upstream_gene_variant 0.11
clpC1 4039091 c.1614G>T synonymous_variant 0.18
clpC1 4039144 c.1560dupG frameshift_variant 0.17
clpC1 4040159 c.546G>T synonymous_variant 0.25
panD 4044035 p.Asp83Tyr missense_variant 0.12
embC 4241382 p.Gly507Val missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Leu missense_variant 0.13
embA 4244082 p.Ala284Thr missense_variant 0.29
embA 4244492 c.1260G>T synonymous_variant 0.29
embA 4245035 c.1805delA frameshift_variant 0.25
embA 4246110 p.Arg960Trp missense_variant 0.18
embB 4247323 c.810G>T synonymous_variant 0.12
embB 4247519 p.Leu336Met missense_variant 0.25
embB 4249193 p.Pro894Thr missense_variant 0.15
aftB 4266972 p.Gly622Val missense_variant 0.15
aftB 4267693 c.1143delG frameshift_variant 0.15
aftB 4267763 c.1074C>A synonymous_variant 0.15
aftB 4269153 c.-317C>A upstream_gene_variant 0.22
whiB6 4338378 p.Glu48Asp missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408459 c.-257G>T upstream_gene_variant 0.13
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0