TB-Profiler result

Run: ERR2229180
Summary

Run ID: ERR2229180

Sample name:

Date: 31-03-2023 16:46:51

Number of reads: 359706

Percentage reads mapped: 99.61

Strain: lineage4

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
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
pncA 2289067 p.Ser59Pro missense_variant 0.14 pyrazinamide
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 5984 p.Arg249Cys missense_variant 0.2
gyrB 6329 p.Glu364Lys missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9077 c.1776C>A synonymous_variant 0.12
mshA 575623 c.276C>A synonymous_variant 0.33
ccsA 619836 c.-55A>C upstream_gene_variant 0.67
rpoB 760417 p.Ala204Val missense_variant 0.14
rpoB 761626 p.Arg607Leu missense_variant 0.2
rpoC 763474 p.Asn35Lys missense_variant 0.2
rpoC 763705 c.336G>A synonymous_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775967 p.Met838Ile missense_variant 0.4
mmpL5 776319 p.Ser721Thr missense_variant 0.25
mmpL5 777380 c.1101G>T synonymous_variant 0.25
mmpL5 778432 p.Arg17Trp missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781567 p.Thr3Asn missense_variant 0.22
rplC 800615 c.-194G>T upstream_gene_variant 0.15
fbiC 1302892 c.-39C>A upstream_gene_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303953 c.1023C>T synonymous_variant 0.4
fbiC 1304101 c.1171C>A synonymous_variant 0.12
Rv1258c 1406196 p.Ala382Glu missense_variant 0.17
Rv1258c 1406689 p.Phe218Val missense_variant 0.5
Rv1258c 1407185 p.Met52Ile missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472890 n.1045C>A non_coding_transcript_exon_variant 0.15
rrs 1473017 n.1172A>G non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673810 p.Ser124Leu missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918625 p.Pro229Gln missense_variant 0.29
ndh 2103017 p.Ala9Glu missense_variant 0.22
PPE35 2167746 p.Thr956Ser missense_variant 0.17
PPE35 2167814 c.2799C>T synonymous_variant 0.19
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.17
PPE35 2169272 c.1341C>G synonymous_variant 0.17
PPE35 2169278 c.1335T>C synonymous_variant 0.18
PPE35 2169281 c.1332T>G synonymous_variant 0.17
PPE35 2169287 c.1326T>C synonymous_variant 0.15
PPE35 2169293 c.1320T>C synonymous_variant 0.17
PPE35 2169308 c.1305C>T synonymous_variant 0.18
PPE35 2169902 p.Leu237Phe missense_variant 0.25
PPE35 2169910 p.Asn235Tyr missense_variant 0.38
PPE35 2169939 p.Gly225Ala missense_variant 0.2
PPE35 2169941 c.672C>T synonymous_variant 0.2
PPE35 2169944 c.669G>C synonymous_variant 0.18
PPE35 2169947 c.666T>C synonymous_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.13
PPE35 2170053 p.Thr187Ser missense_variant 0.18
PPE35 2170371 p.Thr81Val missense_variant 0.14
PPE35 2170385 c.228G>T synonymous_variant 0.13
PPE35 2170392 p.Gly74Ala missense_variant 0.14
PPE35 2170400 c.213G>C synonymous_variant 0.29
PPE35 2170412 c.201G>A synonymous_variant 0.15
PPE35 2170415 c.198A>G synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986754 c.-85G>T upstream_gene_variant 0.22
ald 3086690 c.-130G>T upstream_gene_variant 0.18
fbiD 3338944 c.-174G>T upstream_gene_variant 0.12
fbiD 3338947 c.-171G>A upstream_gene_variant 0.12
fprA 3475043 p.Gly346Asp missense_variant 0.5
Rv3236c 3612159 p.Arg320Trp missense_variant 1.0
fbiA 3640475 c.-68C>A upstream_gene_variant 0.2
fbiB 3642570 p.Glu346* stop_gained 0.5
rpoA 3877644 p.Asn288Lys missense_variant 0.2
clpC1 4038357 p.Asp783Gly missense_variant 0.12
clpC1 4038898 p.Gly603Ser missense_variant 0.25
clpC1 4039031 c.1674T>C synonymous_variant 0.29
clpC1 4039645 p.His354Asp missense_variant 0.15
clpC1 4039654 p.Thr351Ser missense_variant 0.17
clpC1 4040144 c.561G>C synonymous_variant 0.22
embC 4240162 c.300C>T synonymous_variant 0.67
embC 4241537 p.Gly559Cys missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.4
embB 4246548 p.Pro12Gln missense_variant 0.57
embB 4246555 c.42G>C synonymous_variant 0.57
embB 4246556 p.Ala15Pro missense_variant 0.57
embB 4246563 p.Leu17Trp missense_variant 0.4
embB 4246567 c.54G>T synonymous_variant 0.4
embB 4249162 c.2649C>T synonymous_variant 0.33
embB 4249168 c.2655C>T synonymous_variant 0.29
aftB 4267346 p.Asn497Lys missense_variant 0.25
ethR 4326961 c.-588G>C upstream_gene_variant 0.33
ethR 4326964 c.-585G>A upstream_gene_variant 0.33
ethR 4326970 c.-579G>T upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0