TB-Profiler result

Run: SRR7131129
Summary

Run ID: SRR7131129

Sample name:

Date: 04-04-2023 18:46:17

Number of reads: 1320148

Percentage reads mapped: 99.99

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 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777527 c.954G>A synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407278 c.63G>C synonymous_variant 0.12
Rv1258c 1407286 p.Ala19Ser missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.12
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.15
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.15
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.11
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.11
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.11
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.11
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.11
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.11
rrs 1472583 n.738T>C non_coding_transcript_exon_variant 0.11
rrl 1475979 n.2322T>A non_coding_transcript_exon_variant 0.1
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.12
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.13
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.14
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.14
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.14
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.14
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.14
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.12
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.12
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.12
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.12
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.21
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.2
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.23
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.23
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.18
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.18
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.18
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.18
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.19
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.16
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102321 p.Val241Ala missense_variant 0.11
PPE35 2168297 c.2315delC frameshift_variant 0.11
PPE35 2170436 c.176delG frameshift_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.44
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0