TB-Profiler result

Run: SRR4036003
Summary

Run ID: SRR4036003

Sample name:

Date: 04-04-2023 07:26:11

Number of reads: 1499317

Percentage reads mapped: 98.58

Strain: lineage4.4.1.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
lineage4.4.1.1.1 Euro-American S;Orphans 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
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 9304 p.Gly668Asp missense_variant 1.0
ccsA 620140 p.Ala84Thr missense_variant 0.11
rpoB 763056 p.Thr1084Ala missense_variant 0.11
rpoC 763710 p.Leu114Pro missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778820 p.Arg29His missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474088 n.434delC non_coding_transcript_exon_variant 0.29
rrl 1475032 n.1375G>T non_coding_transcript_exon_variant 0.22
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.15
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.15
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.16
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.2
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.24
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.29
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.31
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.36
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.29
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2167990 c.2622delC frameshift_variant 0.17
PPE35 2169320 p.Leu431Phe missense_variant 0.3
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223150 c.15G>T synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289665 c.-424G>T upstream_gene_variant 0.12
thyA 3073806 c.666C>G synonymous_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474979 p.Arg325Cys missense_variant 0.13
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3641575 c.43delC frameshift_variant 0.13
clpC1 4039488 p.Ala406Val missense_variant 0.14
embC 4242425 p.Arg855Gly missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249621 c.3108G>C synonymous_variant 0.12
aftB 4267913 c.924G>A synonymous_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0