TB-Profiler result

Run: SRR19428606
Summary

Run ID: SRR19428606

Sample name:

Date: 03-04-2023 21:42:21

Number of reads: 743741

Percentage reads mapped: 99.57

Strain: lineage4.9.1;lineage4.3.4.2;lineage4.3.3

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 0.83
lineage4.9 Euro-American (H37Rv-like) T1 None 0.11
lineage4.9.1 Euro-American (H37Rv-like) T1 None 0.06
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.47
lineage4.3.4 Euro-American (LAM) LAM RD174 0.33
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.38
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 6817 c.-485G>A upstream_gene_variant 0.3
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.95
gyrA 8040 p.Gly247Ser missense_variant 0.45
gyrA 8978 c.1677C>T synonymous_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 0.76
fgd1 491529 p.Trp249* stop_gained 0.13
rpoB 760895 c.1089C>T synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 0.1
rpoC 763884 p.Ala172Val missense_variant 0.14
rpoC 763886 c.517C>A synonymous_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 0.93
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472718 n.873C>A non_coding_transcript_exon_variant 0.18
rrl 1473680 n.23G>T non_coding_transcript_exon_variant 0.14
rrl 1474954 n.1297A>C non_coding_transcript_exon_variant 0.5
rrl 1475078 n.1421T>C non_coding_transcript_exon_variant 0.2
rrl 1475492 n.1835C>A non_coding_transcript_exon_variant 0.12
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.56
rrl 1476077 n.2420T>A non_coding_transcript_exon_variant 0.22
rrl 1476287 n.2630A>G non_coding_transcript_exon_variant 0.14
rrl 1476775 n.3118A>T non_coding_transcript_exon_variant 0.11
rrl 1476776 n.3119C>A non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168171 p.Ile814Met missense_variant 0.1
PPE35 2170048 p.Leu189Val missense_variant 0.16
PPE35 2170053 p.Thr187Ser missense_variant 0.16
Rv1979c 2222308 p.Asp286Gly missense_variant 0.17
Rv1979c 2223051 p.Glu38Asp missense_variant 0.59
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289138 p.Leu35Arg missense_variant 0.16
kasA 2518132 c.18C>T synonymous_variant 0.13
kasA 2518919 p.Gly269Ser missense_variant 0.51
Rv2752c 3065824 p.Pro123Leu missense_variant 0.45
thyA 3073868 p.Thr202Ala missense_variant 0.83
ald 3086788 c.-32T>C upstream_gene_variant 0.97
ald 3087897 p.Gly360Trp missense_variant 0.12
fbiD 3339385 p.Asp90Asn missense_variant 0.18
Rv3083 3448714 p.Asp71His missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.9
fprA 3474244 p.Gly80Arg missense_variant 0.11
fprA 3474597 c.591C>A synonymous_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 0.13
Rv3236c 3612009 p.Ala370Thr missense_variant 0.34
clpC1 4038287 c.2418C>T synonymous_variant 0.82
embC 4239763 c.-100C>T upstream_gene_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 0.85
embB 4246999 c.486C>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 0.87