TB-Profiler result

Run: ERR11050212
Summary

Run ID: ERR11050212

Sample name:

Date: 02-04-2023 16:10:44

Number of reads: 607140

Percentage reads mapped: 99.43

Strain: lineage4.2.2.2

Drug-resistance: Sensitive

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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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.98
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR 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
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 5239 c.-1C>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9448 p.Val716Asp missense_variant 0.12
fgd1 490756 c.-27T>G upstream_gene_variant 0.18
fgd1 490959 c.177C>T synonymous_variant 0.15
mshA 576077 c.730C>T synonymous_variant 1.0
mshA 576336 p.Pro330Leu missense_variant 0.12
mshA 576442 p.Cys365Trp missense_variant 0.25
rpoB 761484 p.Gly560Arg missense_variant 0.23
rpoC 764094 p.Arg242His missense_variant 0.13
rpoC 764367 p.Gly333Ala missense_variant 0.31
rpoC 765223 c.1854G>A synonymous_variant 0.12
rpoC 766973 p.Ala1202Pro missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776613 p.Leu623Pro missense_variant 0.11
mmpL5 777127 p.Ser452Arg missense_variant 0.18
mmpS5 778632 p.Leu92Val missense_variant 0.29
mmpR5 779096 p.Ala36Val missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801408 c.600C>T synonymous_variant 0.14
fbiC 1305012 c.2082G>C synonymous_variant 0.57
embR 1416430 c.918G>C synonymous_variant 0.33
embR 1417430 c.-83C>T upstream_gene_variant 0.12
atpE 1461104 c.60C>G synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472260 n.415G>A non_coding_transcript_exon_variant 1.0
rrs 1472546 n.701G>T non_coding_transcript_exon_variant 0.22
rrl 1473980 n.323A>C non_coding_transcript_exon_variant 0.15
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.26
fabG1 1674065 p.Lys209Thr missense_variant 0.27
rpsA 1834831 c.1290G>T synonymous_variant 0.13
tlyA 1918084 p.Thr49Pro missense_variant 0.4
ndh 2102817 p.Leu76Val missense_variant 0.17
katG 2154301 p.Leu604Ser missense_variant 0.11
katG 2154663 p.Phe483Leu missense_variant 0.2
katG 2155518 p.Trp198Cys missense_variant 0.29
katG 2156470 c.-360delT upstream_gene_variant 0.18
PPE35 2168382 p.Phe744Tyr missense_variant 0.33
PPE35 2170037 c.576C>G synonymous_variant 0.4
PPE35 2170069 p.Pro182Ala missense_variant 1.0
PPE35 2170386 p.Leu76Arg missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288980 p.Ser88Ala missense_variant 0.17
pncA 2289900 c.-659A>G upstream_gene_variant 0.11
kasA 2519172 p.Leu353His missense_variant 0.18
eis 2714761 p.Leu191Gln missense_variant 0.27
eis 2714852 p.Ser161Gly missense_variant 0.29
eis 2715291 c.42G>C synonymous_variant 0.14
folC 2746578 p.Arg341Cys missense_variant 0.18
pepQ 2859933 c.486C>G synonymous_variant 0.4
Rv2752c 3065216 p.Ile326Val missense_variant 0.17
Rv2752c 3065602 p.Asp197Ala missense_variant 0.33
Rv2752c 3065675 p.Phe173Ile missense_variant 0.25
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
thyX 3067545 p.Glu134Ala missense_variant 0.18
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339053 c.-65G>C upstream_gene_variant 0.58
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568769 c.-90A>G upstream_gene_variant 0.15
whiB7 3568872 c.-193C>T upstream_gene_variant 0.22
Rv3236c 3612811 c.306G>C synonymous_variant 0.18
fbiB 3641679 p.Thr49Ser missense_variant 0.18
alr 3840395 c.1026C>T synonymous_variant 0.13
clpC1 4040254 p.Ala151Thr missense_variant 1.0
clpC1 4040545 p.Ile54Phe missense_variant 0.3
panD 4043935 p.Asp116Gly missense_variant 0.2
panD 4043952 c.330T>G synonymous_variant 0.22
embC 4240430 p.Gly190Arg missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244473 p.Val414Gly missense_variant 0.29
embA 4244508 p.Leu426Val missense_variant 0.25
embA 4245765 p.Glu845Gln missense_variant 0.15
embB 4246527 p.Ala5Gly missense_variant 0.33
embB 4248328 c.1815G>C synonymous_variant 0.42
embB 4249151 p.Ala880Thr missense_variant 0.14
embB 4249755 p.Gly1081Ala missense_variant 0.33
aftB 4267148 p.Glu563Asp missense_variant 0.25
aftB 4267400 c.1437G>C synonymous_variant 0.4
aftB 4268440 p.Asp133His missense_variant 0.13
ethA 4328409 c.-936T>G upstream_gene_variant 0.25
ethA 4328415 c.-942A>G upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407620 p.Tyr195Asn missense_variant 0.29
gid 4407673 p.Val177Gly missense_variant 0.33