TB-Profiler result

Run: SRR4035793
Summary

Run ID: SRR4035793

Sample name:

Date: 04-04-2023 07:18:06

Number of reads: 1424797

Percentage reads mapped: 99.39

Strain: lineage4.1.2

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
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 6469 c.-833T>C upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9232 p.Arg644Leu missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 576028 c.681T>A synonymous_variant 0.13
mshA 576671 c.1324C>A synonymous_variant 0.14
ccsA 619745 c.-146A>G upstream_gene_variant 0.14
ccsA 620029 p.Leu47Met missense_variant 0.14
ccsA 620095 p.His69Asn missense_variant 0.15
ccsA 620667 p.Trp259Cys missense_variant 0.17
rpoB 759775 c.-32_-31insT upstream_gene_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760234 p.Ser143Asn missense_variant 0.14
rpoB 761401 p.Arg532His missense_variant 0.2
rpoC 763436 p.Trp23Arg missense_variant 0.11
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764428 c.1059G>A synonymous_variant 0.15
rpoC 764430 p.Leu354Pro missense_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765670 p.His767Gln missense_variant 0.14
rpoC 766891 c.3527delT frameshift_variant 0.13
rpoC 766901 p.Gly1178Ser missense_variant 0.14
rpoC 766954 c.3585C>A synonymous_variant 0.14
rpoC 767066 p.Leu1233Met missense_variant 0.18
rpoC 767175 p.Asn1269Ile missense_variant 0.15
rpoC 767186 p.Gln1273* stop_gained 0.14
rpoC 767264 p.Ala1299Thr missense_variant 0.14
rpoC 767315 p.Arg1316Ser missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777338 c.1142delA frameshift_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800743 c.-66C>G upstream_gene_variant 0.11
rplC 801067 p.Asp87Asn missense_variant 0.15
fbiC 1302805 c.-126C>T upstream_gene_variant 0.15
fbiC 1303110 c.180G>C synonymous_variant 0.11
fbiC 1303473 c.543G>A synonymous_variant 0.15
fbiC 1305043 p.Ser705Thr missense_variant 0.18
fbiC 1305161 p.Phe744Ser missense_variant 0.11
Rv1258c 1407375 c.-35A>G upstream_gene_variant 0.1
embR 1416605 p.Arg248Leu missense_variant 0.15
embR 1416934 c.414G>C synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674172 p.Met245Val missense_variant 0.11
rpsA 1834541 p.Pro334Ser missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102925 p.Ile40Phe missense_variant 0.13
PPE35 2170088 c.525G>T synonymous_variant 0.18
Rv1979c 2222500 p.Ala222Gly missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288789 c.453G>A synonymous_variant 0.13
pncA 2290080 c.-839T>C upstream_gene_variant 0.12
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2715526 c.-194C>A upstream_gene_variant 0.15
eis 2715536 c.-204C>T upstream_gene_variant 0.14
folC 2746161 p.Thr480Pro missense_variant 0.13
folC 2746313 c.1285delC frameshift_variant 0.25
folC 2746935 p.Arg222Trp missense_variant 0.15
folC 2746971 p.Ala210Pro missense_variant 0.14
pepQ 2859496 p.Ile308Thr missense_variant 0.22
pepQ 2859641 p.Gly260Ser missense_variant 0.14
pepQ 2859826 p.Ala198Val missense_variant 0.14
pepQ 2859828 c.591G>A synonymous_variant 0.14
Rv2752c 3065218 p.Ser325Asn missense_variant 0.17
thyX 3067783 p.Ala55Thr missense_variant 0.22
thyA 3073710 c.762T>C synonymous_variant 0.11
thyA 3074042 p.Pro144Ser missense_variant 0.17
thyA 3074062 p.Glu137Gly missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448422 c.-82T>C upstream_gene_variant 0.14
Rv3083 3448549 p.Gly16Ser missense_variant 0.2
Rv3083 3448572 c.69G>A synonymous_variant 0.2
Rv3083 3448889 p.Arg129Leu missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474159 c.153C>G synonymous_variant 0.18
fprA 3475371 c.1365C>A synonymous_variant 0.14
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612857 p.Arg87Leu missense_variant 0.18
Rv3236c 3613238 c.-122C>T upstream_gene_variant 0.2
fbiA 3640812 p.Gln90His missense_variant 0.14
fbiA 3641161 p.Asp207His missense_variant 0.12
fbiB 3641818 p.Thr95Ile missense_variant 0.17
fbiB 3642295 p.Gln254Arg missense_variant 0.12
alr 3840732 p.Glu230Gly missense_variant 0.12
clpC1 4038168 p.Ala846Val missense_variant 0.15
clpC1 4039946 c.759A>G synonymous_variant 0.11
panD 4044340 c.-59G>A upstream_gene_variant 0.13
embC 4240161 p.Thr100Ile missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243158 c.-75G>C upstream_gene_variant 0.12
embA 4243180 c.-53C>A upstream_gene_variant 0.14
embA 4244408 c.1176G>A synonymous_variant 0.14
embA 4244789 p.Phe519Leu missense_variant 0.15
embA 4245597 p.Lys789Glu missense_variant 0.2
embB 4245617 c.-897C>T upstream_gene_variant 0.22
embB 4245926 c.-588C>A upstream_gene_variant 0.14
embA 4246114 p.Val961Asp missense_variant 0.13
embA 4246136 p.Gln968His missense_variant 0.15
embB 4246531 c.18C>T synonymous_variant 0.2
embB 4247880 p.Val456Glu missense_variant 0.13
embB 4248419 c.1906C>T synonymous_variant 0.12
embB 4248653 p.Met714Val missense_variant 0.2
embB 4248956 p.Trp815Arg missense_variant 0.12
embB 4249750 p.Glu1079Asp missense_variant 0.1
aftB 4267165 p.Trp558Arg missense_variant 0.13
aftB 4267224 p.Ile538Asn missense_variant 0.12
aftB 4267269 p.His523Arg missense_variant 0.1
aftB 4267998 p.Leu280Ser missense_variant 0.12
aftB 4268846 c.-10G>C upstream_gene_variant 0.11
aftB 4269783 c.-947G>T upstream_gene_variant 0.2
ubiA 4269815 p.Thr7Ser missense_variant 0.15
ubiA 4269863 c.-30C>A upstream_gene_variant 0.14
ethA 4326273 p.Phe401Leu missense_variant 0.11
ethA 4326693 p.Arg261Trp missense_variant 0.14
ethA 4327337 p.Asp46Ala missense_variant 0.11
ethA 4327421 p.Ser18Asn missense_variant 0.13
ethA 4327486 c.-13A>G upstream_gene_variant 0.12
ethR 4327853 p.Met102Thr missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408334 c.-132G>C upstream_gene_variant 0.13