TB-Profiler result

Run: ERR2229585
Summary

Run ID: ERR2229585

Sample name:

Date: 31-03-2023 17:20:19

Number of reads: 785089

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
fgd1 491560 p.His260Asn missense_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.38
mshA 576438 p.Ala364Val missense_variant 0.14
ccsA 619999 p.Ala37Pro missense_variant 0.29
ccsA 620024 p.Ala45Glu missense_variant 0.25
rpoC 762707 c.-663G>A upstream_gene_variant 0.2
rpoB 762765 p.Leu987Met missense_variant 0.17
rpoC 764239 c.871delC frameshift_variant 0.18
rpoC 765639 p.Glu757Val missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775867 p.Arg872Cys missense_variant 0.18
mmpL5 776208 p.Leu758Arg missense_variant 0.25
mmpL5 776830 p.His551Asn missense_variant 0.11
mmpL5 777482 c.999G>A synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406390 p.Leu317Phe missense_variant 0.18
Rv1258c 1406673 p.Arg223Gln missense_variant 0.12
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.12
Rv1258c 1406946 p.Ala132Gly missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673884 p.Asn149Asp missense_variant 0.2
inhA 1674473 p.Val91Ala missense_variant 0.2
rpsA 1833927 p.Thr129Arg missense_variant 0.22
rpsA 1834081 c.540C>T synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101659 p.Ala462Thr missense_variant 0.18
ndh 2102921 p.Lys41Arg missense_variant 0.17
katG 2155805 p.Ile103Phe missense_variant 0.14
katG 2155817 p.Gly99Trp missense_variant 0.17
PPE35 2167868 c.2745A>C synonymous_variant 0.11
PPE35 2167941 p.Ser891Ile missense_variant 0.11
PPE35 2168084 p.Glu843Asp missense_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169029 p.Asp528Glu missense_variant 0.43
PPE35 2169219 p.Leu465Gln missense_variant 0.17
PPE35 2169602 c.1011C>A synonymous_variant 0.2
PPE35 2169890 c.723C>T synonymous_variant 0.12
PPE35 2169893 c.720C>A synonymous_variant 0.19
PPE35 2169902 p.Leu237Phe missense_variant 0.22
PPE35 2169910 p.Asn235Tyr missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.54
PPE35 2170053 p.Thr187Ser missense_variant 0.58
PPE35 2170189 p.Glu142Gln missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714781 c.552G>A synonymous_variant 0.22
folC 2746564 c.1035A>G synonymous_variant 0.15
Rv2752c 3064923 c.1269C>T synonymous_variant 0.13
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474923 p.Asp306Gly missense_variant 0.11
fprA 3475285 p.Asp427Asn missense_variant 0.18
fbiB 3641568 p.Ile12Phe missense_variant 0.2
fbiB 3642464 c.930A>G synonymous_variant 0.17
alr 3840488 c.933G>T synonymous_variant 0.12
alr 3841363 p.Thr20Ala missense_variant 0.13
rpoA 3878141 c.342_366delCGGCGTCACCGTGCACAACCCCGGC frameshift_variant 0.18
rpoA 3878174 p.Pro112Thr missense_variant 0.11
clpC1 4039207 p.Thr500Ser missense_variant 0.11
clpC1 4039829 p.Leu292Phe missense_variant 0.15
embC 4242039 p.Ala726Val missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243463 c.231G>C synonymous_variant 0.11
embA 4244991 p.Val587Ile missense_variant 0.15
embA 4245402 p.Thr724Pro missense_variant 0.2
embA 4245957 p.Gly909Trp missense_variant 0.17
embA 4246232 c.3001delG frameshift_variant 0.2
embB 4246328 c.-186C>T upstream_gene_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.18
embB 4246569 p.Ala19Gly missense_variant 0.29
aftB 4268640 p.Leu66Gln missense_variant 0.17
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0