TB-Profiler result

Run: ERR2229424
Summary

Run ID: ERR2229424

Sample name:

Date: 31-03-2023 17:10:30

Number of reads: 703190

Percentage reads mapped: 99.43

Strain: lineage4.8

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
lineage4.8 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
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 7233 p.Arg665His missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575942 p.Arg199Ser missense_variant 0.12
mshA 576079 c.732G>T synonymous_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.27
mshA 576144 p.Arg266Leu missense_variant 0.22
rpoB 759723 c.-84C>T upstream_gene_variant 0.14
rpoB 759726 c.-81A>T upstream_gene_variant 0.14
rpoB 759727 c.-80A>T upstream_gene_variant 0.14
rpoB 759730 c.-77A>G upstream_gene_variant 0.14
rpoB 759733 c.-74_-73insGTTTCGGC upstream_gene_variant 0.15
rpoB 763033 p.Ala1076Asp missense_variant 0.12
rpoC 764078 p.Asp237Tyr missense_variant 0.22
rpoC 764484 p.Arg372Gln missense_variant 0.17
rpoC 764532 p.Gly388Ala missense_variant 0.22
rpoC 767122 c.3753C>T synonymous_variant 0.12
mmpL5 775615 p.Ala956Thr missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776172 p.Asp770Val missense_variant 0.12
mmpL5 776174 c.2307C>A synonymous_variant 0.12
mmpR5 778457 c.-533C>T upstream_gene_variant 0.15
mmpR5 779242 p.Val85Phe missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801355 p.His183Tyr missense_variant 0.12
fbiC 1303549 p.Val207Leu missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304994 c.2066delT frameshift_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473823 n.166T>A non_coding_transcript_exon_variant 0.25
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475512 n.1855G>T non_coding_transcript_exon_variant 0.22
rrl 1476167 n.2512delA non_coding_transcript_exon_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.4
rpsA 1833694 c.153G>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101932 p.Ala371Thr missense_variant 0.18
ndh 2102203 c.840T>C synonymous_variant 0.12
ndh 2102637 p.Pro136Thr missense_variant 0.5
katG 2153892 c.2220C>A synonymous_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.21
PPE35 2169281 c.1332T>G synonymous_variant 0.21
PPE35 2170283 c.330G>C synonymous_variant 0.12
PPE35 2170371 p.Thr81Val missense_variant 0.12
PPE35 2170392 p.Gly74Ala missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289802 c.-561G>T upstream_gene_variant 0.25
pncA 2289873 c.-632C>A upstream_gene_variant 0.12
kasA 2519226 p.Leu371Arg missense_variant 0.22
eis 2714885 p.His150Asn missense_variant 0.12
eis 2715001 p.Ser111Tyr missense_variant 0.13
folC 2746525 c.1074G>A synonymous_variant 0.13
pepQ 2860165 p.Gly85Ala missense_variant 0.15
ribD 2987067 p.Leu77Phe missense_variant 0.18
ribD 2987105 c.267C>A synonymous_variant 0.22
ribD 2987290 p.Asp151Val missense_variant 0.18
Rv2752c 3065026 p.Arg389Gln missense_variant 0.15
Rv2752c 3065305 p.Ala296Val missense_variant 0.13
Rv2752c 3067079 c.-888C>A upstream_gene_variant 0.18
thyA 3074006 p.Asp156Tyr missense_variant 0.13
thyA 3074436 c.36C>A synonymous_variant 0.15
fbiD 3339160 p.Ala15Thr missense_variant 0.14
fbiD 3339615 c.498G>A synonymous_variant 0.15
fbiD 3339749 p.Val211Gly missense_variant 0.25
Rv3236c 3612800 p.Val106Ala missense_variant 0.18
Rv3236c 3612868 c.249C>A synonymous_variant 0.18
fbiA 3641181 c.640delT frameshift_variant 0.14
alr 3840240 p.Pro394Gln missense_variant 0.15
alr 3840323 p.Phe366Leu missense_variant 0.17
alr 3840627 p.Ala265Asp missense_variant 0.18
rpoA 3878194 p.Val105Ala missense_variant 0.11
ddn 3987245 p.Gln134His missense_variant 0.13
clpC1 4039526 c.1179G>C synonymous_variant 0.3
clpC1 4039530 p.Asp392Ala missense_variant 0.3
clpC1 4040409 p.Gly99Val missense_variant 0.29
embC 4239693 c.-170G>A upstream_gene_variant 0.13
embC 4241830 c.1968G>A synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243902 p.Leu224Met missense_variant 0.17
embA 4244659 p.Leu476Pro missense_variant 0.17
embA 4245850 p.Ala873Glu missense_variant 0.2
embA 4246406 p.Glu1058Asp missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4249368 p.Asp952Gly missense_variant 0.25
aftB 4267693 p.Ile382Val missense_variant 0.11
aftB 4269780 c.-944C>G upstream_gene_variant 0.12
ethA 4326281 p.Val398Ala missense_variant 0.13
ethR 4326961 c.-588G>C upstream_gene_variant 0.13
ethR 4326964 c.-585G>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0