TB-Profiler result

Run: ERR245824
Summary

Run ID: ERR245824

Sample name:

Date: 31-03-2023 18:23:01

Number of reads: 1699014

Percentage reads mapped: 99.59

Strain: lineage4.3.4.2.1

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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7504 p.Arg68Pro missense_variant 0.38
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8445 p.Arg382Gly missense_variant 0.21
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.22
rpoB 759831 p.Thr9Pro missense_variant 0.29
rpoB 762249 p.Leu815Val missense_variant 0.3
rpoC 764725 p.Phe452Leu missense_variant 0.28
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765082 c.1713G>C synonymous_variant 0.38
rpoC 766628 p.Arg1087Gly missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407489 c.-149G>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.19
fabG1 1673449 p.Thr4Pro missense_variant 0.24
fabG1 1673546 p.Ala36Gly missense_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.15
katG 2154036 p.Ser692Arg missense_variant 0.39
katG 2154615 c.1497G>C synonymous_variant 0.4
PPE35 2167871 c.2742G>C synonymous_variant 0.22
PPE35 2169320 p.Leu431Phe missense_variant 0.22
PPE35 2169866 c.747G>C synonymous_variant 0.35
PPE35 2170156 p.Ala153Pro missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289293 c.-52C>G upstream_gene_variant 0.36
kasA 2518891 c.777C>A synonymous_variant 0.4
eis 2714366 p.Val323Leu missense_variant 0.5
ahpC 2725954 c.-239C>T upstream_gene_variant 0.38
ahpC 2726756 c.564C>G synonymous_variant 0.48
folC 2746186 c.1413G>C synonymous_variant 0.4
folC 2747555 p.Thr15Asn missense_variant 0.18
pepQ 2859381 c.1038C>G synonymous_variant 0.25
pepQ 2859832 p.Ala196Gly missense_variant 0.3
ribD 2987392 p.Arg185Pro missense_variant 0.22
Rv2752c 3064552 p.Arg547Pro missense_variant 0.24
Rv2752c 3064836 p.Leu452Phe missense_variant 0.33
Rv2752c 3065265 c.927C>G synonymous_variant 0.19
Rv2752c 3065618 p.Gly192Arg missense_variant 0.17
thyX 3067965 c.-20C>G upstream_gene_variant 0.29
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087362 p.Tyr181* stop_gained 0.31
Rv3083 3448929 p.Tyr142* stop_gained 0.14
Rv3083 3449673 p.Tyr390* stop_gained 0.44
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Gly missense_variant 0.25
fprA 3474942 p.Glu312Asp missense_variant 0.27
fprA 3475280 p.Val425Gly missense_variant 0.5
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612425 p.Ala231Gly missense_variant 0.29
fbiA 3641271 p.Tyr243* stop_gained 0.29
fbiB 3642772 p.Asp413Ala missense_variant 0.67
alr 3840494 c.927G>C synonymous_variant 0.25
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3877766 p.Ala248Pro missense_variant 0.38
ddn 3987013 p.Gly57Ala missense_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039363 p.Ala448Pro missense_variant 0.35
clpC1 4039932 p.Gly258Val missense_variant 0.4
embC 4239870 p.Thr3Asn missense_variant 0.2
embC 4241056 c.1194C>G synonymous_variant 0.27
embC 4241128 c.1266G>C synonymous_variant 0.4
embC 4241429 p.Phe523Val missense_variant 0.71
embC 4241456 p.Ala532Pro missense_variant 0.57
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243977 p.Ala249Pro missense_variant 0.4
embA 4244539 p.Ala436Glu missense_variant 0.29
embB 4246805 p.Val98Leu missense_variant 0.25
embB 4247603 p.Leu364Val missense_variant 0.22
embB 4248725 p.Ser738Ala missense_variant 0.5
ubiA 4269529 p.Ala102Gly missense_variant 0.11
ubiA 4269857 c.-24A>C upstream_gene_variant 0.18
ethA 4327672 c.-199G>A upstream_gene_variant 0.46
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0