TB-Profiler result

Run: SRR4037649

Summary

Run ID: SRR4037649

Sample name:

Date: 04-04-2023 07:34:19

Number of reads: 472168

Percentage reads mapped: 99.65

Strain: lineage4.4.1.1

Drug-resistance: Other


Download CSV Download TXT Download PDF Download JSON
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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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
ethA 4326292 c.1181delA frameshift_variant 0.29 ethionamide
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 7624 p.Pro108Gln missense_variant 0.13
gyrA 8159 c.858G>T synonymous_variant 0.12
gyrA 8722 p.Arg474Leu missense_variant 0.22
gyrA 8951 c.1650G>A synonymous_variant 0.11
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619981 p.Leu31Met missense_variant 0.2
rpoB 759851 c.45G>T synonymous_variant 0.22
rpoB 759887 c.81C>A synonymous_variant 0.17
rpoB 762745 p.Gln980Arg missense_variant 0.4
rpoB 763167 p.Glu1121* stop_gained 0.2
rpoC 765589 c.2220G>T synonymous_variant 0.22
rpoC 766073 p.Ala902Thr missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416443 p.Pro302Gln missense_variant 0.2
atpE 1461016 c.-29C>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472083 n.238G>A non_coding_transcript_exon_variant 0.14
rrl 1474841 n.1184G>T non_coding_transcript_exon_variant 0.17
rrl 1475690 n.2033G>T non_coding_transcript_exon_variant 0.14
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.15
fabG1 1673167 c.-273G>T upstream_gene_variant 0.25
inhA 1673363 c.-839G>A upstream_gene_variant 1.0
fabG1 1674076 p.Thr213Pro missense_variant 0.4
inhA 1674300 c.99C>A synonymous_variant 0.18
rpsA 1834201 c.660C>A synonymous_variant 0.29
rpsA 1834958 p.Leu473Met missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918500 c.561G>T synonymous_variant 0.12
ndh 2102107 c.936C>A synonymous_variant 0.22
ndh 2102640 p.Ala135Thr missense_variant 0.2
ndh 2102990 p.Val18Ala missense_variant 0.8
katG 2154687 c.1425C>A synonymous_variant 0.2
katG 2154729 p.Gln461His missense_variant 0.2
katG 2154817 p.Pro432His missense_variant 0.25
PPE35 2168015 c.2598C>A synonymous_variant 0.22
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2169964 p.Leu217Ile missense_variant 0.25
PPE35 2169970 p.Gly215Ser missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289339 c.-98C>A upstream_gene_variant 0.15
eis 2714259 c.1074C>T synonymous_variant 0.4
eis 2714487 c.846C>A synonymous_variant 0.25
eis 2715354 c.-22G>A upstream_gene_variant 0.12
ahpC 2726236 p.Leu15Pro missense_variant 0.17
folC 2747662 c.-64G>C upstream_gene_variant 0.22
Rv2752c 3065745 c.447C>A synonymous_variant 0.17
Rv2752c 3066175 p.Pro6Arg missense_variant 1.0
thyA 3074250 c.222G>A synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338952 c.-166C>A upstream_gene_variant 0.18
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3448768 p.Ala89Thr missense_variant 0.14
Rv3083 3449545 p.Leu348Met missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474448 c.445delC frameshift_variant 0.25
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3640647 c.-888G>A upstream_gene_variant 0.18
alr 3840823 p.Ala200Thr missense_variant 0.12
rpoA 3877890 c.618C>T synonymous_variant 0.18
clpC1 4039093 p.Gly538Trp missense_variant 0.15
clpC1 4039948 p.Gly253* stop_gained 0.25
panD 4044082 p.Gly67Asp missense_variant 0.17
embC 4241940 p.Pro693Gln missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245035 c.1803C>A synonymous_variant 0.13
embB 4247726 p.Glu405Tyr missense_variant 0.15
embB 4247767 c.1254G>T synonymous_variant 0.25
embB 4249196 p.Gly895Trp missense_variant 0.25
aftB 4267042 p.Arg599Ser missense_variant 0.29
aftB 4268168 c.669C>A synonymous_variant 0.18
ubiA 4269631 p.Ala68Val missense_variant 0.33
ethA 4326018 p.Pro486Thr missense_variant 0.25
ethA 4326422 p.Gly351Val missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408124 p.Ala27Ser missense_variant 0.25