TB-Profiler result

Run: SRR19428608
Summary

Run ID: SRR19428608

Sample name:

Date: 03-04-2023 21:42:10

Number of reads: 1112574

Percentage reads mapped: 99.76

Strain: lineage4.3.4.2.1;lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 0.25
lineage4 Euro-American LAM;T;S;X;H None 0.81
lineage4.3 Euro-American (LAM) mainly-LAM None 0.78
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.32
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.21
lineage4.3.4 Euro-American (LAM) LAM RD174 0.8
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.76
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.79
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 6140 p.Val301Leu missense_variant 0.78
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7635 p.Gly112Ser missense_variant 0.73
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.27
rpoB 759746 c.-61C>T upstream_gene_variant 0.15
rpoC 762434 c.-936T>G upstream_gene_variant 0.36
rpoC 763031 c.-339T>C upstream_gene_variant 0.38
rpoC 764995 c.1626C>G synonymous_variant 0.76
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.32
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473895 n.238C>A non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>A non_coding_transcript_exon_variant 0.33
rrl 1474157 n.500G>T non_coding_transcript_exon_variant 0.22
rrl 1474858 n.1201C>T non_coding_transcript_exon_variant 0.15
rrl 1474984 n.1327G>A non_coding_transcript_exon_variant 0.15
rrl 1475218 n.1561C>A non_coding_transcript_exon_variant 0.22
rrl 1475231 n.1574C>A non_coding_transcript_exon_variant 0.2
rrl 1475615 n.1958C>T non_coding_transcript_exon_variant 0.33
rrl 1475658 n.2001G>T non_coding_transcript_exon_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 0.98
katG 2154724 p.Arg463Leu missense_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 0.14
PPE35 2170461 p.Gly51Glu missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.29
pncA 2289365 c.-125delC upstream_gene_variant 0.19
ahpC 2726105 c.-88G>A upstream_gene_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 0.81
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.72
alr 3840719 c.702A>G synonymous_variant 0.78
clpC1 4038287 c.2418C>T synonymous_variant 0.81
embC 4240172 p.Val104Met missense_variant 0.23
embC 4241562 p.Arg567His missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249439 p.Glu976Lys missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.11
gid 4408156 p.Leu16Arg missense_variant 0.77
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0