TB-Profiler result

Run: ERR4812871
Summary

Run ID: ERR4812871

Sample name:

Date: 01-04-2023 12:23:38

Number of reads: 637017

Percentage reads mapped: 99.27

Strain: lineage4

Drug-resistance: MDR-TB

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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
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289009 p.Gly78Val missense_variant 0.17 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 5787 p.Thr183Met missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8379 p.Gln360* stop_gained 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490834 p.Arg18Cys missense_variant 0.15
fgd1 490854 c.72C>A synonymous_variant 0.17
fgd1 491115 c.333G>T synonymous_variant 0.25
mshA 576091 c.744C>A synonymous_variant 0.2
mshA 576123 p.Leu259Arg missense_variant 0.29
rpoB 761358 p.Val518Ile missense_variant 0.17
rpoB 762832 p.Ser1009Ile missense_variant 0.18
rpoC 762887 c.-483G>T upstream_gene_variant 0.13
rpoC 762944 c.-426C>A upstream_gene_variant 0.14
rpoC 764868 p.Arg500His missense_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406307 p.Arg345His missense_variant 0.33
embR 1416955 p.Phe131Leu missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673431 c.-771G>A upstream_gene_variant 1.0
inhA 1674838 p.Ala213Thr missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154037 p.Ser692Ile missense_variant 0.14
katG 2154461 p.Ala551Thr missense_variant 0.12
PPE35 2168078 c.2535C>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289156 p.Arg29Pro missense_variant 1.0
kasA 2518185 p.Ser24Leu missense_variant 0.12
kasA 2518790 p.Ala226Thr missense_variant 0.29
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2747750 c.-152G>T upstream_gene_variant 0.22
pepQ 2860507 c.-89C>A upstream_gene_variant 0.13
ribD 2987583 p.Gly249Ser missense_variant 0.15
Rv2752c 3066234 c.-43G>T upstream_gene_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074205 p.Glu89Asp missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087221 c.402C>T synonymous_variant 0.14
Rv3083 3448406 c.-98G>T upstream_gene_variant 0.25
Rv3083 3448864 p.Val121Met missense_variant 0.22
Rv3083 3448975 c.472C>A synonymous_variant 0.12
fprA 3473958 c.-49C>A upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474721 p.Ala239Ser missense_variant 0.15
fprA 3474730 p.Gly242Cys missense_variant 0.15
Rv3236c 3612158 p.Arg320Gln missense_variant 0.22
ddn 3986998 p.Thr52Ile missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040784 c.-80C>A upstream_gene_variant 0.11
panD 4044329 c.-48C>T upstream_gene_variant 0.17
embC 4240123 c.261C>A synonymous_variant 0.13
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4243181 c.-52C>T upstream_gene_variant 0.2
embA 4243262 c.30C>T synonymous_variant 0.15
embA 4246195 p.Pro988His missense_variant 0.14
embB 4246850 p.Ala113Ser missense_variant 1.0
embB 4247280 p.Phe256Ser missense_variant 0.14
embB 4248813 p.Leu767Pro missense_variant 0.22
embB 4249684 p.Trp1057* stop_gained 0.13
aftB 4268613 p.Gly75Val missense_variant 0.29
aftB 4268852 c.-16G>A upstream_gene_variant 0.22
ubiA 4269710 p.Gly42Cys missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407973 p.Val77Gly missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0