TB-Profiler result

Run: ERR245815
Summary

Run ID: ERR245815

Sample name:

Date: 31-03-2023 18:22:45

Number of reads: 2373516

Percentage reads mapped: 99.53

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 Euro-American (LAM) mainly-LAM 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 0.99
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575309 c.-39C>G upstream_gene_variant 0.33
mshA 575932 p.Glu195Asp missense_variant 0.2
mshA 576184 c.837A>C synonymous_variant 0.45
ccsA 620407 p.Pro173Ala missense_variant 0.23
rpoB 759620 c.-187A>C upstream_gene_variant 0.41
rpoC 762836 c.-534C>G upstream_gene_variant 0.2
rpoC 764905 p.Phe512Leu missense_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765082 c.1713G>C synonymous_variant 0.23
rpoC 765338 p.Gln657Glu missense_variant 0.21
rpoC 767083 c.3714C>T synonymous_variant 1.0
rpoC 767305 p.Tyr1312* stop_gained 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304445 c.1515G>C synonymous_variant 0.25
embR 1417136 p.Ser71Ile missense_variant 0.29
embR 1417233 c.115C>T synonymous_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.28
fabG1 1673449 p.Thr4Pro missense_variant 0.33
fabG1 1673546 p.Ala36Gly missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918377 c.438T>G synonymous_variant 0.2
PPE35 2169866 c.747G>C synonymous_variant 0.56
PPE35 2170156 p.Ala153Pro missense_variant 0.75
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714355 c.978C>G synonymous_variant 0.27
eis 2714366 p.Val323Leu missense_variant 0.18
ahpC 2725954 c.-239C>T upstream_gene_variant 0.43
ahpC 2726756 c.564C>G synonymous_variant 0.22
folC 2746186 c.1413G>C synonymous_variant 0.33
folC 2747263 c.336C>A synonymous_variant 0.16
pepQ 2859381 c.1038C>G synonymous_variant 0.24
pepQ 2859680 p.Leu247Val missense_variant 0.4
Rv2752c 3064741 p.Gly484Ala missense_variant 0.33
Rv2752c 3064836 p.Leu452Phe missense_variant 0.33
thyX 3067531 p.Ala139Pro missense_variant 0.29
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448929 p.Tyr142* stop_gained 0.36
Rv3083 3449058 p.Ser185Arg missense_variant 0.31
Rv3083 3449673 p.Tyr390* stop_gained 0.32
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Gly missense_variant 0.26
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiA 3641271 p.Tyr243* stop_gained 0.5
fbiA 3641534 p.Ala331Gly missense_variant 0.33
fbiB 3641955 p.Gly141Arg missense_variant 0.27
fbiB 3642033 p.Ala167Pro missense_variant 0.29
alr 3840494 c.927G>C synonymous_variant 0.5
alr 3840520 p.Ala301Pro missense_variant 0.31
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3840869 c.552C>G synonymous_variant 1.0
rpoA 3878238 p.Asp90Glu missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039932 p.Gly258Val missense_variant 0.25
embC 4239870 p.Thr3Asn missense_variant 0.29
embC 4240646 p.Phe262Val missense_variant 0.2
embC 4241128 c.1266G>C synonymous_variant 0.38
embC 4241429 p.Phe523Val missense_variant 0.44
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.2
embA 4243730 c.498G>A synonymous_variant 0.58
embA 4244375 c.1143C>G synonymous_variant 0.4
embA 4244460 p.Val410Leu missense_variant 0.27
embB 4247284 c.771G>T synonymous_variant 0.11
embB 4248725 p.Ser738Ala missense_variant 0.4
ubiA 4269529 p.Ala102Gly missense_variant 0.4
ethA 4327672 c.-199G>A upstream_gene_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0