TB-Profiler result

Run: ERR4820115
Summary

Run ID: ERR4820115

Sample name:

Date: 01-04-2023 16:29:40

Number of reads: 898171

Percentage reads mapped: 99.44

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8534 c.1233G>A synonymous_variant 1.0
gyrA 8834 c.1533C>A synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490901 p.His40Arg missense_variant 0.11
fgd1 491021 p.Arg80His missense_variant 0.14
fgd1 491075 p.Pro98Arg missense_variant 0.18
fgd1 491423 p.Gly214Val missense_variant 0.22
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576278 p.Gly311Arg missense_variant 0.2
ccsA 619910 p.Asn7Ser missense_variant 0.22
ccsA 620623 p.Ile245Leu missense_variant 0.25
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761439 p.Asp545Tyr missense_variant 0.14
rpoB 761801 c.1995G>T synonymous_variant 0.15
rpoC 763453 c.89delA frameshift_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779260 p.Thr91Pro missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303329 c.399C>T synonymous_variant 1.0
fbiC 1303842 c.912C>A synonymous_variant 0.22
fbiC 1304204 p.Ala425Gly missense_variant 0.33
Rv1258c 1406693 c.648G>T synonymous_variant 0.18
Rv1258c 1406724 p.Gln206Pro missense_variant 0.18
Rv1258c 1406872 p.Gly157Ser missense_variant 0.17
Rv1258c 1407057 p.Gly95Val missense_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471944 n.99G>A non_coding_transcript_exon_variant 0.12
inhA 1674855 c.654C>A synonymous_variant 0.12
rpsA 1833916 c.375C>A synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101683 p.Gly454Ser missense_variant 0.12
ndh 2102447 p.Gly199Asp missense_variant 0.14
ndh 2102895 p.Leu50Met missense_variant 0.12
katG 2153929 p.Trp728* stop_gained 0.15
katG 2154855 p.Asp419Glu missense_variant 0.33
katG 2155090 p.Trp341* stop_gained 0.12
katG 2155685 p.Lys143* stop_gained 0.11
PPE35 2168246 c.2367C>G synonymous_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518877 p.Lys255* stop_gained 0.15
kasA 2519171 p.Leu353Ile missense_variant 0.12
kasA 2519329 c.1215C>A synonymous_variant 0.22
eis 2714935 p.Pro133Arg missense_variant 0.15
thyX 3067915 p.Leu11Met missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339436 p.Ala107Thr missense_variant 0.12
fbiD 3339539 p.Ala141Asp missense_variant 0.12
fbiD 3339556 p.Gly147Ser missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474133 p.Pro43Thr missense_variant 0.13
Rv3236c 3612714 c.403C>A synonymous_variant 0.11
fbiA 3640354 c.-189C>T upstream_gene_variant 1.0
clpC1 4038209 c.2496G>A synonymous_variant 0.11
clpC1 4039051 p.Ala552Thr missense_variant 0.12
panD 4043938 p.Ile115Asn missense_variant 0.18
panD 4043986 p.Arg99Leu missense_variant 0.14
embC 4240656 p.Ala265Val missense_variant 0.13
embC 4240730 p.Asn290His missense_variant 0.15
embC 4241053 c.1191G>T synonymous_variant 0.4
embC 4241590 p.Phe576Leu missense_variant 0.12
embC 4241874 p.Leu671Gln missense_variant 0.14
embC 4242144 p.Pro761Arg missense_variant 0.12
embA 4242511 c.-722G>T upstream_gene_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245564 p.Gly778Ser missense_variant 0.13
aftB 4267386 p.His484Arg missense_variant 0.18
aftB 4267404 p.Pro478Leu missense_variant 0.25
aftB 4268121 p.Thr239Ile missense_variant 0.14
ethA 4326045 p.Gly477Cys missense_variant 0.14
ethA 4326927 p.Ser183Gly missense_variant 0.14
ethA 4327217 p.Lys86Arg missense_variant 0.13
ethR 4327580 p.Leu11Pro missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0