TB-Profiler result

Run: SRR6789633
Summary

Run ID: SRR6789633

Sample name:

Date: 04-04-2023 16:04:31

Number of reads: 648980

Percentage reads mapped: 94.51

Strain: lineage4.9.1

Drug-resistance: Other

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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
lineage4.9 Euro-American (H37Rv-like) T1 None 1.0
lineage4.9.1 Euro-American (H37Rv-like) T1 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
embB 4247652 p.Ser380Asn missense_variant 0.12 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 6751 c.-551G>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8978 c.1677C>T synonymous_variant 0.91
ccsA 619697 c.-194A>G upstream_gene_variant 0.12
ccsA 619725 c.-166C>G upstream_gene_variant 0.12
rpoB 760180 p.Ala125Asp missense_variant 0.18
rpoB 762278 c.2472C>A synonymous_variant 0.14
rpoC 763502 p.Gly45Ser missense_variant 0.12
rpoC 763536 p.Arg56Leu missense_variant 0.13
rpoC 763829 p.Glu154* stop_gained 0.22
rpoC 764315 p.Ala316Thr missense_variant 0.13
rpoC 765523 c.2154C>T synonymous_variant 0.12
rpoC 766408 c.3039C>G synonymous_variant 0.2
rpoC 766411 c.3042C>G synonymous_variant 0.18
rpoC 766426 c.3057C>T synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778220 c.-770G>T upstream_gene_variant 0.2
mmpS5 778493 p.Phe138Tyr missense_variant 0.22
mmpS5 778686 p.Leu74Phe missense_variant 0.12
mmpS5 778697 p.Asn70Ser missense_variant 0.13
mmpS5 778846 p.Ile20Met missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801299 p.Thr164Asn missense_variant 0.13
fbiC 1302779 c.-152C>T upstream_gene_variant 0.14
Rv1258c 1406088 p.Ala418Asp missense_variant 0.15
Rv1258c 1406674 p.Arg223Trp missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.1
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
inhA 1674366 c.165G>T synonymous_variant 0.12
inhA 1674415 p.Ala72Thr missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155351 p.Arg254His missense_variant 0.15
katG 2155664 p.Pro150Ser missense_variant 0.14
katG 2155773 p.Tyr113* stop_gained 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.61
PPE35 2170053 p.Thr187Ser missense_variant 0.61
PPE35 2170574 c.39C>T synonymous_variant 0.14
Rv1979c 2222744 p.Phe141Val missense_variant 0.13
Rv1979c 2223145 p.Arg7Lys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289138 p.Leu35Arg missense_variant 1.0
pncA 2289188 c.54G>T synonymous_variant 0.12
pncA 2289196 p.Gly16Cys missense_variant 0.12
pncA 2289294 c.-53G>T upstream_gene_variant 0.12
kasA 2518348 c.234A>T synonymous_variant 0.17
kasA 2518532 p.Leu140Met missense_variant 0.18
kasA 2518743 p.Phe210Ser missense_variant 0.5
folC 2746584 p.Leu339Val missense_variant 0.25
pepQ 2859364 p.Pro352His missense_variant 0.12
pepQ 2859702 p.Leu239Phe missense_variant 0.15
Rv2752c 3064944 c.1248G>A synonymous_variant 0.22
Rv2752c 3065209 p.Leu328Ser missense_variant 0.13
thyX 3067337 c.609C>T synonymous_variant 0.5
thyA 3073955 p.Gly173Arg missense_variant 0.11
thyA 3074424 c.48G>A synonymous_variant 0.13
ald 3087574 p.Asn252Ser missense_variant 0.12
fbiD 3339385 p.Asp90Asn missense_variant 1.0
Rv3083 3449357 p.Asn285Thr missense_variant 0.22
fprA 3474803 p.Arg266His missense_variant 0.22
Rv3236c 3612339 p.Arg260Cys missense_variant 0.12
fbiA 3640730 p.Asp63Gly missense_variant 0.13
fbiA 3640828 p.Gly96Arg missense_variant 0.12
fbiA 3641249 p.Ala236Glu missense_variant 0.12
fbiB 3642326 c.792C>G synonymous_variant 0.13
fbiB 3642516 p.Ala328Thr missense_variant 0.17
alr 3840271 p.Gly384Cys missense_variant 0.14
alr 3841507 c.-87C>A upstream_gene_variant 0.11
rpoA 3878706 c.-199G>A upstream_gene_variant 0.12
clpC1 4038245 p.Phe820Leu missense_variant 0.25
clpC1 4039799 c.906C>A synonymous_variant 0.11
panD 4044148 c.133delA frameshift_variant 0.15
panD 4044362 c.-81T>C upstream_gene_variant 0.17
embC 4239807 c.-56G>A upstream_gene_variant 0.14
embC 4241609 p.Pro583Thr missense_variant 0.33
embC 4242843 p.Gln994Arg missense_variant 0.15
embA 4243000 c.-233C>A upstream_gene_variant 0.11
embA 4243794 p.Arg188Ser missense_variant 0.17
embA 4245031 p.Arg600Gln missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.17
embB 4246666 c.153G>A synonymous_variant 0.29
embB 4248641 p.Val710Leu missense_variant 0.17
embB 4249003 c.2490G>T synonymous_variant 0.14
aftB 4267717 p.Ala374Ser missense_variant 0.14
aftB 4268124 p.Ser238Asn missense_variant 0.14
ubiA 4269296 p.Met180Val missense_variant 0.12
ethA 4326788 p.Leu229Pro missense_variant 0.2
ethR 4328140 p.Arg198Ser missense_variant 0.15
whiB6 4338325 p.Ala66Gly missense_variant 0.15
whiB6 4338331 p.Arg64Leu missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0