TB-Profiler result

Run: ERR2229587
Summary

Run ID: ERR2229587

Sample name:

Date: 31-03-2023 17:20:17

Number of reads: 478270

Percentage reads mapped: 99.11

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 7618 p.Arg106Leu missense_variant 0.12
gyrA 8866 p.Glu522Ala missense_variant 0.25
gyrA 8968 p.Ala556Val missense_variant 0.22
gyrA 9416 c.2115C>T synonymous_variant 0.18
fgd1 490649 c.-134C>T upstream_gene_variant 0.17
mshA 575564 p.Leu73Met missense_variant 0.18
mshA 576517 c.1171delT frameshift_variant 0.29
mshA 576630 p.Phe428Ser missense_variant 0.25
ccsA 619707 c.-184T>C upstream_gene_variant 0.22
ccsA 620485 p.Arg199Ser missense_variant 0.67
rpoB 760114 c.311delC frameshift_variant 0.22
rpoB 760361 c.555T>C synonymous_variant 0.13
rpoB 762497 p.Asp897Glu missense_variant 0.33
rpoC 766655 p.Glu1096Gln missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776417 c.2064G>C synonymous_variant 0.14
mmpL5 777127 p.Ser452Gly missense_variant 0.29
mmpL5 778397 p.Ile28Met missense_variant 0.14
mmpL5 778762 c.-282G>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781899 p.Arg114Ser missense_variant 1.0
rplC 800716 c.-93T>C upstream_gene_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305080 p.Arg717Gln missense_variant 0.17
embR 1417176 p.Ala58Thr missense_variant 0.2
atpE 1460955 c.-90T>A upstream_gene_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474841 n.1184G>T non_coding_transcript_exon_variant 0.29
rrl 1475159 n.1502G>C non_coding_transcript_exon_variant 0.29
rrl 1475250 n.1593C>A non_coding_transcript_exon_variant 0.33
rrl 1475439 n.1782A>T non_coding_transcript_exon_variant 0.25
rrl 1475868 n.2211G>A non_coding_transcript_exon_variant 0.15
inhA 1674581 p.Tyr127Phe missense_variant 0.33
rpsA 1834116 p.Glu192Gly missense_variant 0.25
rpsA 1834397 p.His286Asn missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918279 p.Gly114* stop_gained 0.18
ndh 2102080 c.963C>A synonymous_variant 0.4
katG 2154406 p.Pro569Gln missense_variant 0.14
katG 2155108 p.Ile335Asn missense_variant 0.33
PPE35 2167784 c.2829C>T synonymous_variant 0.22
PPE35 2167865 c.2748G>C synonymous_variant 0.23
PPE35 2167868 c.2745A>C synonymous_variant 0.23
PPE35 2167878 p.Ser912Asn missense_variant 0.17
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 0.27
PPE35 2169281 c.1332T>G synonymous_variant 0.27
PPE35 2169287 c.1326T>C synonymous_variant 0.27
PPE35 2169394 p.Ala407Thr missense_variant 0.25
PPE35 2169397 p.Gly406Ser missense_variant 0.25
PPE35 2169732 p.Asn294Ser missense_variant 0.22
PPE35 2169748 p.Ile289Phe missense_variant 0.25
PPE35 2169749 c.864A>C synonymous_variant 0.25
PPE35 2169754 p.Phe287Ile missense_variant 0.38
PPE35 2169762 p.Ile284Gly missense_variant 0.25
PPE35 2169767 c.846A>G synonymous_variant 0.33
PPE35 2169770 c.843T>C synonymous_variant 0.33
PPE35 2169773 c.840C>T synonymous_variant 0.33
PPE35 2169902 p.Leu237Phe missense_variant 0.21
PPE35 2169910 p.Asn235Tyr missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.62
PPE35 2170053 p.Thr187Ser missense_variant 0.54
Rv1979c 2221745 p.Val474Leu missense_variant 0.18
Rv1979c 2221852 p.Phe438Tyr missense_variant 0.2
Rv1979c 2222378 p.Val263Ile missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726251 p.Gly20Val missense_variant 0.25
thyX 3067908 p.Ala13Asp missense_variant 0.22
ald 3087177 p.Val120Leu missense_variant 0.17
ald 3087876 p.Glu353Lys missense_variant 0.22
Rv3236c 3612273 p.Val282Phe missense_variant 0.17
fbiA 3640454 c.-88delC upstream_gene_variant 0.4
fbiB 3642512 p.Leu326Phe missense_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.54
ddn 3987269 c.426C>A synonymous_variant 0.15
clpC1 4039714 p.Tyr331His missense_variant 0.21
clpC1 4039730 c.975C>G synonymous_variant 0.17
clpC1 4039768 p.Ala313Ser missense_variant 0.15
embC 4239816 c.-47A>T upstream_gene_variant 0.2
embC 4241241 p.Leu460Pro missense_variant 0.14
embC 4242046 c.2184T>A synonymous_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247094 p.Gly194Glu missense_variant 0.29
embB 4247116 c.603G>T synonymous_variant 0.25
aftB 4269318 c.-482G>C upstream_gene_variant 0.22
ubiA 4269985 c.-152T>C upstream_gene_variant 0.29
ethR 4326961 c.-588G>C upstream_gene_variant 0.15
ethR 4326964 c.-585G>A upstream_gene_variant 0.15
ethR 4326970 c.-579G>T upstream_gene_variant 0.15
ethA 4327541 c.-68G>A upstream_gene_variant 0.18
ethR 4327819 p.Ala91Ser missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407916 p.Arg96Leu missense_variant 0.17
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0