TB-Profiler result

Run: SRR10315584

Summary

Run ID: SRR10315584

Sample name:

Date: 02-04-2023 17:11:06

Number of reads: 5851325

Percentage reads mapped: 99.17

Strain: lineage4.4.1.1

Drug-resistance: Pre-XDR-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
lineage4.4 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
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
gyrA 7581 p.Asp94His missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Phe missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4326801 c.672dupG frameshift_variant 1.0 ethionamide, ethionamide
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin
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 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474498 n.841G>A non_coding_transcript_exon_variant 0.13
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.11
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.11
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.14
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.17
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.17
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.25
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.2
rrl 1474869 n.1212G>A non_coding_transcript_exon_variant 0.2
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.2
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.2
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.2
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.1
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.12
rrl 1476117 n.2460G>T non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
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
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267361 c.1476C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0