TB-Profiler result

Run: SRR4033964
Summary

Run ID: SRR4033964

Sample name:

Date: 04-04-2023 06:28:32

Number of reads: 939508

Percentage reads mapped: 99.69

Strain: lineage4.3.2.1

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
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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 5520 p.Pro94Leu missense_variant 1.0
gyrB 6897 p.Arg553Gln missense_variant 0.14
gyrA 7222 c.-80C>T upstream_gene_variant 0.78
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7631 c.330G>C synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9315 c.2014C>T synonymous_variant 0.17
rpoB 760036 p.Val77Ala missense_variant 0.14
rpoB 761673 p.Gly623Trp missense_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766667 p.Ser1100Pro missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304600 p.Ile557Ser missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471666 n.-180A>C upstream_gene_variant 1.0
rrs 1471912 n.67G>A non_coding_transcript_exon_variant 0.18
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rpsA 1834344 p.Asp268Val missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101736 p.Ala436Gly missense_variant 0.1
Rv1979c 2223266 c.-102G>T upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519197 c.1083G>A synonymous_variant 0.2
ahpC 2726293 p.Tyr34Cys missense_variant 1.0
folC 2747215 c.383delA frameshift_variant 0.2
folC 2747713 c.-115C>T upstream_gene_variant 0.13
thyX 3067422 p.Leu175Pro missense_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 0.93
thyA 3074575 c.-104G>A upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087200 c.385delC frameshift_variant 0.14
fbiD 3339039 c.-79G>A upstream_gene_variant 0.11
fbiD 3339273 c.156T>G synonymous_variant 0.18
Rv3083 3448945 p.Gly148Cys missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475300 p.Ala432Thr missense_variant 0.2
fbiB 3642200 c.666G>A synonymous_variant 0.15
fbiB 3642563 c.1029C>T synonymous_variant 0.11
fbiB 3642827 c.1293G>A synonymous_variant 0.25
rpoA 3877604 c.903delG frameshift_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240589 p.Ala243Ser missense_variant 0.12
embC 4241244 c.1384delC frameshift_variant 0.18
embC 4241320 c.1458G>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244099 c.867T>C synonymous_variant 0.1
embB 4246544 p.Thr11Pro missense_variant 0.2
embB 4249536 p.Glu1008Ala missense_variant 0.17
aftB 4268032 p.Pro269Thr missense_variant 0.17
ethA 4326665 p.Arg270Pro missense_variant 0.17
ethA 4327989 c.-516G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0