TB-Profiler result

Run: SRR5535692
Summary

Run ID: SRR5535692

Sample name:

Date: 04-04-2023 10:37:51

Number of reads: 837241

Percentage reads mapped: 99.13

Strain: lineage4

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
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
ethA 4326831 p.Gln215* stop_gained 0.2 ethionamide
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 5167 c.-73C>A upstream_gene_variant 0.67
gyrB 5963 p.Ala242Ser missense_variant 0.25
gyrB 6864 p.Thr542Lys missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7396 p.Ala32Val missense_variant 0.29
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8011 p.Ser237Tyr missense_variant 0.4
gyrA 8109 p.Val270Leu missense_variant 0.4
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9332 p.Asn677Lys missense_variant 0.2
fgd1 491271 c.489C>T synonymous_variant 0.29
mshA 575314 c.-34C>A upstream_gene_variant 0.22
mshA 575420 p.Thr25Ser missense_variant 0.25
mshA 576404 p.Glu353* stop_gained 0.29
ccsA 620286 c.396G>T synonymous_variant 0.67
rpoB 760585 p.Asn260Ser missense_variant 0.12
rpoB 761526 p.Asp574Asn missense_variant 0.29
rpoB 761787 c.1981C>A synonymous_variant 0.25
rpoC 763136 c.-234C>A upstream_gene_variant 0.29
rpoC 764810 p.Pro481Thr missense_variant 0.18
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765337 p.Trp656Cys missense_variant 0.14
rpoC 765515 p.Leu716Ile missense_variant 0.29
rpoC 765784 c.2415C>A synonymous_variant 0.22
rpoC 765808 p.Gln813His missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778382 c.-608C>A upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781763 c.204C>T synonymous_variant 0.25
rplC 801102 c.294G>C synonymous_variant 0.33
rplC 801318 p.Met170Ile missense_variant 0.5
fbiC 1303247 p.Thr106Met missense_variant 0.13
fbiC 1303508 p.Pro193Gln missense_variant 0.33
fbiC 1303767 p.Lys279Asn missense_variant 0.67
fbiC 1304220 c.1290G>T synonymous_variant 0.29
fbiC 1305306 c.2376A>G synonymous_variant 0.25
Rv1258c 1406834 c.507C>A synonymous_variant 0.33
embR 1417140 p.Ala70Ser missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475193 n.1536C>A non_coding_transcript_exon_variant 0.5
rrl 1475962 n.2305G>T non_coding_transcript_exon_variant 0.5
fabG1 1673249 c.-191C>T upstream_gene_variant 1.0
inhA 1673586 c.-616C>A upstream_gene_variant 0.25
inhA 1674460 p.Lys87Gln missense_variant 0.25
inhA 1674770 p.Ala190Asp missense_variant 0.22
inhA 1674833 p.Ala211Asp missense_variant 0.29
rpsA 1833409 c.-133C>A upstream_gene_variant 0.22
rpsA 1833664 c.123C>T synonymous_variant 0.5
rpsA 1834362 p.Leu274Ser missense_variant 0.4
tlyA 1917823 c.-117C>A upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917990 c.51G>T synonymous_variant 0.25
ndh 2101880 p.Ser388Ile missense_variant 0.33
katG 2155958 p.Pro52Thr missense_variant 0.13
katG 2156344 c.-233C>A upstream_gene_variant 0.4
PPE35 2168499 p.Ser705* stop_gained 1.0
PPE35 2168558 c.2055C>A synonymous_variant 0.4
PPE35 2170319 p.Glu98Asp missense_variant 0.5
PPE35 2170355 c.258G>T synonymous_variant 0.67
pncA 2289432 c.-191C>A upstream_gene_variant 0.14
pncA 2289633 c.-392G>T upstream_gene_variant 0.33
eis 2714309 p.Pro342Thr missense_variant 0.67
eis 2714444 p.Arg297Ser missense_variant 0.18
eis 2714829 c.504C>A synonymous_variant 0.25
eis 2715049 p.Gly95Asp missense_variant 0.18
folC 2746767 p.Gln278Glu missense_variant 1.0
folC 2747022 p.Val193Ile missense_variant 1.0
folC 2747780 c.-182C>T upstream_gene_variant 0.33
pepQ 2859647 p.Gln258Lys missense_variant 0.4
pepQ 2860151 p.Ala90Thr missense_variant 0.22
ribD 2987420 c.582C>T synonymous_variant 0.14
Rv2752c 3064527 c.1665C>A synonymous_variant 0.4
Rv2752c 3064878 c.1314C>A synonymous_variant 0.25
Rv2752c 3064944 c.1248G>T synonymous_variant 0.25
Rv2752c 3065278 p.Thr305Ile missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339457 p.Gln114* stop_gained 0.5
Rv3083 3448894 p.Tyr131Asp missense_variant 1.0
Rv3083 3448924 p.Gly141Cys missense_variant 0.5
Rv3083 3449342 p.Ser280Phe missense_variant 0.29
Rv3083 3449642 p.Asn380Ser missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474319 p.Gly105Cys missense_variant 0.4
fprA 3474433 p.Pro143Thr missense_variant 0.5
fprA 3474619 p.Ala205Ser missense_variant 0.17
fprA 3474712 p.Glu236* stop_gained 0.29
fbiA 3641164 p.Ile208Val missense_variant 1.0
fbiB 3642597 p.Asp355Tyr missense_variant 0.2
rpoA 3878130 c.378C>A synonymous_variant 0.25
rpoA 3878149 p.Asn120Thr missense_variant 0.2
rpoA 3878304 c.204G>T synonymous_variant 0.29
clpC1 4038230 p.Lys825Asn missense_variant 0.25
clpC1 4038337 p.Leu790Ile missense_variant 0.17
clpC1 4039927 p.Arg260Cys missense_variant 0.25
panD 4044223 p.Leu20Arg missense_variant 0.22
embC 4240068 p.Ser69Ile missense_variant 0.2
embC 4240359 p.Ala166Asp missense_variant 0.33
embC 4241415 p.Arg518His missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242665 p.Ala935Ser missense_variant 0.2
embC 4242672 p.Pro937Gln missense_variant 0.22
embA 4245352 p.Lys707Met missense_variant 0.5
embA 4246236 p.Leu1002Ile missense_variant 0.5
embB 4246584 p.Arg24Leu missense_variant 0.33
embB 4246586 p.Gly25Trp missense_variant 0.33
embB 4247807 p.Ala432Ser missense_variant 0.25
embB 4248122 p.Leu537Met missense_variant 0.25
embB 4249024 c.2511C>A synonymous_variant 0.29
aftB 4267131 p.Pro569Leu missense_variant 1.0
ubiA 4269238 p.Ala199Asp missense_variant 0.4
ubiA 4269541 p.Pro98His missense_variant 0.29
ubiA 4269623 p.Leu71Ile missense_variant 0.2
ubiA 4269713 p.Gly41Arg missense_variant 0.22
ethA 4326075 p.Leu467Ile missense_variant 0.2
ethA 4326896 p.Ala193Glu missense_variant 0.2
ethA 4327206 p.Ala90Thr missense_variant 0.67
ethA 4327475 c.-2C>A upstream_gene_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338674 c.-153G>A upstream_gene_variant 1.0