TB-Profiler result

Run: SRR5007172
Summary

Run ID: SRR5007172

Sample name:

Date: 04-04-2023 07:51:54

Number of reads: 2579863

Percentage reads mapped: 99.21

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
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 1472494 n.649A>G non_coding_transcript_exon_variant 0.22
rrs 1472496 n.651T>A non_coding_transcript_exon_variant 0.25
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.25
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.25
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.25
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.33
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.43
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.43
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.5
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.5
rrl 1474674 n.1017A>C non_coding_transcript_exon_variant 0.5
rrl 1474675 n.1018C>A non_coding_transcript_exon_variant 0.5
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.5
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.5
rrl 1474694 n.1037C>T non_coding_transcript_exon_variant 0.67
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.67
rrl 1474717 n.1060_1061insGTGAG non_coding_transcript_exon_variant 0.67
rrl 1474723 n.1066G>A non_coding_transcript_exon_variant 0.67
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 0.67
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.67
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.67
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.67
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.67
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.67
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.67
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.67
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.67
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.67
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.14
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.11
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102506 c.537C>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245786 p.Ala852Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0