TB-Profiler result

Run: SRR2101440

Summary

Run ID: SRR2101440

Sample name:

Date: 03-04-2023 23:43:08

Number of reads: 452641

Percentage reads mapped: 99.56

Strain: lineage4.1.1

Drug-resistance: RR-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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
embB 4247325 p.Ala271Val missense_variant 0.12 ethambutol
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 6574 c.-728C>T upstream_gene_variant 0.14
gyrA 6922 c.-380G>T upstream_gene_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7914 p.Leu205Val missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491683 p.Val301Met missense_variant 0.14
rpoB 759620 c.-187A>C upstream_gene_variant 0.38
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777211 p.Asp424Asn missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406725 p.Gln206Lys missense_variant 0.12
embR 1416394 c.954C>A synonymous_variant 0.11
embR 1416976 c.372C>T synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472866 n.1021C>A non_coding_transcript_exon_variant 0.25
rrs 1473224 n.1379G>A non_coding_transcript_exon_variant 1.0
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.22
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.4
rrl 1476731 n.3074G>A non_coding_transcript_exon_variant 0.2
inhA 1674415 c.216delC frameshift_variant 0.11
tlyA 1917806 c.-134T>G upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101850 p.Val398Ala missense_variant 0.1
PPE35 2167863 p.Ser917* stop_gained 0.13
Rv1979c 2222050 p.Leu372Pro missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726651 c.459G>A synonymous_variant 0.1
folC 2746338 p.Ala421Thr missense_variant 0.2
folC 2746341 p.Ala420Thr missense_variant 0.2
folC 2747173 c.426G>A synonymous_variant 0.12
folC 2747784 c.-186C>T upstream_gene_variant 0.13
pepQ 2859623 p.Pro266Ser missense_variant 0.13
thyA 3074645 c.-174T>G upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087413 c.595delA frameshift_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641005 c.464_471delTGATCACC frameshift_variant 0.11
fbiB 3642188 c.654T>C synonymous_variant 1.0
alr 3841168 p.Gly85Cys missense_variant 0.12
rpoA 3878404 p.Gly35Val missense_variant 0.11
clpC1 4039484 c.1221T>G synonymous_variant 0.27
clpC1 4039988 c.717C>A synonymous_variant 0.2
panD 4044217 c.64delT frameshift_variant 0.15
embC 4242594 p.His911Pro missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246650 p.Leu46Pro missense_variant 0.14
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338408 c.114C>A synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338663 c.-142G>T upstream_gene_variant 0.13