TB-Profiler result

Run: ERR2229766

Summary

Run ID: ERR2229766

Sample name:

Date: 31-03-2023 17:34:14

Number of reads: 549919

Percentage reads mapped: 99.16

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8094 p.Gly265Ser missense_variant 0.12
mshA 576368 c.1021C>A synonymous_variant 0.29
mshA 576404 p.Glu353Lys missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.18
mmpL5 776021 c.2460G>C synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800893 p.Val29Phe missense_variant 0.33
fbiC 1302969 c.39G>A synonymous_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
atpE 1460930 c.-115C>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473586 n.-72G>A upstream_gene_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475505 n.1848G>C non_coding_transcript_exon_variant 0.14
rrl 1476162 n.2505A>T non_coding_transcript_exon_variant 0.29
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15
rpsA 1833538 c.-4C>A upstream_gene_variant 0.12
rpsA 1833945 p.Lys135Arg missense_variant 0.25
rpsA 1834297 c.756C>A synonymous_variant 0.18
tlyA 1917816 c.-124G>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918640 p.Ser234Leu missense_variant 0.12
ndh 2101714 p.Glu443Asp missense_variant 0.25
katG 2156525 c.-414T>C upstream_gene_variant 0.11
PPE35 2167745 p.Thr956Arg missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.18
PPE35 2169272 c.1341C>G synonymous_variant 0.18
PPE35 2169278 c.1335T>C synonymous_variant 0.22
PPE35 2169281 c.1332T>G synonymous_variant 0.22
PPE35 2169287 c.1326T>C synonymous_variant 0.19
PPE35 2169293 c.1320T>C synonymous_variant 0.13
PPE35 2169308 c.1305C>T synonymous_variant 0.19
PPE35 2169463 p.Val384Leu missense_variant 0.15
PPE35 2169902 p.Leu237Phe missense_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.37
PPE35 2170053 p.Thr187Ser missense_variant 0.41
PPE35 2170392 p.Gly74Ala missense_variant 0.15
PPE35 2170400 c.213G>C synonymous_variant 0.14
Rv1979c 2222887 p.Tyr93Phe missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518071 c.-44G>T upstream_gene_variant 0.17
kasA 2518192 c.78G>A synonymous_variant 0.15
Rv2752c 3065053 p.Glu380Ala missense_variant 0.13
Rv2752c 3066328 c.-137T>C upstream_gene_variant 0.12
ald 3087250 p.Val144Asp missense_variant 0.12
fbiD 3339324 c.207G>A synonymous_variant 0.12
fbiD 3339480 c.363G>A synonymous_variant 0.18
fbiD 3339678 p.Cys187* stop_gained 0.14
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474143 p.Trp46Tyr missense_variant 0.18
fprA 3474578 p.Ile191Thr missense_variant 0.12
fprA 3475239 c.1233A>G synonymous_variant 0.17
Rv3236c 3612638 p.Phe160Ser missense_variant 0.25
fbiB 3640830 c.-705C>T upstream_gene_variant 0.17
fbiA 3640888 c.349delC frameshift_variant 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.32
rpoA 3878158 c.329_349delTCGTGCCGCCGGCCGGCGTCA disruptive_inframe_deletion 0.18
rpoA 3878182 p.Asp109Gly missense_variant 0.18
ddn 3987290 c.447C>T synonymous_variant 0.13
clpC1 4038617 c.2088G>A synonymous_variant 0.2
clpC1 4039526 c.1179G>C synonymous_variant 0.2
clpC1 4039645 p.His354Asp missense_variant 0.25
clpC1 4039654 p.Thr351Ser missense_variant 0.23
embC 4239893 p.Ala11Ser missense_variant 0.29
embC 4240801 c.939C>T synonymous_variant 0.2
embC 4240803 p.Tyr314Phe missense_variant 0.2
embC 4241455 c.1593C>A synonymous_variant 0.13
embC 4241831 p.Trp657Arg missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243905 p.Asp225Asn missense_variant 0.14
embA 4246200 p.Gln990* stop_gained 0.17
embB 4247761 p.Tyr416* stop_gained 0.12
embB 4249253 p.Gly914Trp missense_variant 0.18
embB 4249297 c.2784G>A synonymous_variant 0.17
aftB 4267082 p.His585Gln missense_variant 0.14
aftB 4267933 p.Ala302Pro missense_variant 0.2
ubiA 4269391 p.Val148Glu missense_variant 0.15
ubiA 4269413 p.Gly141Cys missense_variant 0.14
ethR 4326961 c.-588G>C upstream_gene_variant 0.14
ethR 4326964 c.-585G>A upstream_gene_variant 0.13
ethR 4326970 c.-579G>T upstream_gene_variant 0.12
ethR 4327360 c.-189C>A upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0