TB-Profiler result

Run: SRR4037900

Summary

Run ID: SRR4037900

Sample name:

Date: 04-04-2023 07:45:20

Number of reads: 921015

Percentage reads mapped: 99.67

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 0.99
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 6914 p.Gly559Trp missense_variant 0.14
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7624 p.Pro108Gln missense_variant 0.15
gyrA 7635 p.Gly112Cys missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490594 c.-189C>T upstream_gene_variant 0.15
rpoC 763082 c.-288C>T upstream_gene_variant 0.22
rpoC 763529 p.Pro54Ser missense_variant 0.25
rpoC 763934 p.Ala189Thr missense_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776789 c.1692C>G synonymous_variant 0.13
mmpL5 777217 c.1263delG frameshift_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801258 c.450C>A synonymous_variant 0.13
Rv1258c 1406547 p.Met265Lys missense_variant 0.11
embR 1416809 p.Ala180Val missense_variant 0.14
embR 1417497 c.-150C>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1473906 n.249G>A non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918067 p.Ala43Val missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518957 c.843G>T synonymous_variant 0.17
eis 2714297 p.Ala346Thr missense_variant 0.1
ahpC 2726338 p.Val49Gly missense_variant 0.38
folC 2746463 p.Leu379Pro missense_variant 0.13
Rv2752c 3064775 c.1416delT frameshift_variant 0.33
Rv2752c 3066185 p.Val3Ile missense_variant 0.11
thyX 3067733 c.213G>T synonymous_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4044309 c.-29dupG upstream_gene_variant 0.11
embC 4242425 p.Arg855Gly missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244960 c.1730delT frameshift_variant 0.12
embB 4249354 c.2843_2844dupTG frameshift_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338654 c.-133A>G upstream_gene_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0