TB-Profiler result

Run: SRR5535712
Summary

Run ID: SRR5535712

Sample name:

Date: 04-04-2023 10:38:52

Number of reads: 3424734

Percentage reads mapped: 98.88

Strain: lineage4.4.1.1

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 0.99
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
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
ccsA 620050 p.Val54Met missense_variant 0.18
ccsA 620606 p.Val239Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303836 c.906G>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472635 n.790G>T non_coding_transcript_exon_variant 0.22
rrl 1473956 n.299G>T non_coding_transcript_exon_variant 0.4
rrl 1474517 n.860C>A non_coding_transcript_exon_variant 0.14
rrl 1474848 n.1191G>A non_coding_transcript_exon_variant 0.18
rrl 1475164 n.1507C>A non_coding_transcript_exon_variant 0.2
rrl 1475801 n.2144G>T non_coding_transcript_exon_variant 0.2
rrl 1475824 n.2167G>T non_coding_transcript_exon_variant 0.12
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
kasA 2518636 c.522C>A synonymous_variant 0.13
folC 2747012 p.Pro196Gln missense_variant 0.16
Rv2752c 3065023 p.Pro390Leu missense_variant 1.0
thyX 3067241 c.705G>T synonymous_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448522 p.Val7Phe missense_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474259 p.Gly85Cys missense_variant 0.14
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245563 c.-951G>C upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0