TB-Profiler result

Run: SRR10272571
Summary

Run ID: SRR10272571

Sample name:

Date: 02-04-2023 16:40:38

Number of reads: 854525

Percentage reads mapped: 88.54

Strain: lineage4.4.1.1

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
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
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 6991 p.Asp584Glu missense_variant 0.12
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 491448 c.666C>A synonymous_variant 0.14
mshA 576580 c.1233G>A synonymous_variant 0.13
mshA 576582 p.Pro412Gln missense_variant 0.13
ccsA 620334 c.446_447dupTC frameshift_variant 0.14
rpoC 765552 p.Gly728Val missense_variant 0.13
rpoC 765562 c.2193G>T synonymous_variant 0.12
rpoC 766660 c.3291G>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776154 p.Leu776Ser missense_variant 0.12
mmpL5 776320 p.Ser721Gly missense_variant 0.12
mmpL5 777136 p.Met449Leu missense_variant 0.11
mmpL5 777567 p.Gly305Asp missense_variant 0.12
mmpR5 779078 p.Arg30Met missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473683 n.26G>T non_coding_transcript_exon_variant 0.14
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673349 c.-91G>C upstream_gene_variant 0.12
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
inhA 1674405 p.Glu68Asp missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2153961 p.Gln717His missense_variant 0.15
katG 2154313 p.Lys600Arg missense_variant 0.13
katG 2156436 c.-325C>A upstream_gene_variant 0.12
katG 2156453 c.-342C>A upstream_gene_variant 0.14
PPE35 2169581 c.1032C>G synonymous_variant 0.11
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.6
PPE35 2170053 p.Thr187Ser missense_variant 0.59
Rv1979c 2221985 p.Ile394Val missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517960 c.-155C>A upstream_gene_variant 0.18
kasA 2518410 p.Gly99Asp missense_variant 0.13
kasA 2519140 c.1026G>C synonymous_variant 0.22
kasA 2519143 c.1029G>C synonymous_variant 0.22
kasA 2519153 p.Ile347Val missense_variant 0.22
thyA 3073967 p.Asp169Tyr missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568783 c.-104A>G upstream_gene_variant 0.12
Rv3236c 3612155 p.Arg321Leu missense_variant 1.0
Rv3236c 3612586 c.531C>T synonymous_variant 0.12
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3642512 p.Leu326Phe missense_variant 0.14
alr 3840289 p.Asp378Tyr missense_variant 0.13
alr 3840346 c.1074delC frameshift_variant 0.12
ddn 3986972 p.Lys43Asn missense_variant 0.12
clpC1 4039271 p.Glu478Asp missense_variant 0.12
clpC1 4039420 p.Ala429Thr missense_variant 0.22
clpC1 4039602 p.Ala368Val missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243621 p.Thr130Lys missense_variant 0.13
embB 4247972 p.Thr487Pro missense_variant 0.15
embB 4249690 c.3177C>A synonymous_variant 0.2
aftB 4268658 c.178delT frameshift_variant 0.25
ethR 4327579 p.Leu11Met missense_variant 0.14
ethR 4327897 p.His117Asn missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0