TB-Profiler result

Run: SRR10315660
Summary

Run ID: SRR10315660

Sample name:

Date: 02-04-2023 17:14:38

Number of reads: 6084098

Percentage reads mapped: 97.4

Strain: lineage4.4.1.1.1

Drug-resistance: MDR-TB

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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 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
lineage4.4.1.1.1 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrl 1476471 n.2814G>T non_coding_transcript_exon_variant 0.17 linezolid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289142 p.Tyr34Asp missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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
mshA 576108 p.Ala254Gly missense_variant 0.25
rpoC 766487 p.Pro1040Ser 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 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.67
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.67
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.67
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.67
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.67
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.33
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.33
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.22
rrl 1474522 n.865C>T non_coding_transcript_exon_variant 1.0
rrl 1474810 n.1153G>T non_coding_transcript_exon_variant 0.33
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.25
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.25
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.22
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.46
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.23
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.13
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.27
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.31
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.13
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.16
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.17
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.31
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.25
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.44
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.16
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.16
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.15
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.16
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.16
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.15
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.15
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
Rv2752c 3064993 p.Trp400* stop_gained 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339287 p.Arg57Leu missense_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.38
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0