TB-Profiler result

Run: SRR3732653
Summary

Run ID: SRR3732653

Sample name:

Date: 04-04-2023 05:37:11

Number of reads: 632269

Percentage reads mapped: 99.56

Strain: lineage4

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
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 5067 c.-173A>G upstream_gene_variant 1.0
gyrB 7097 p.Glu620* stop_gained 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9251 c.1950G>C synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575291 c.-57G>T upstream_gene_variant 0.14
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620322 c.432G>A synonymous_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760555 p.Glu250Gly missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765275 p.Arg636Trp missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778238 c.-752C>T upstream_gene_variant 1.0
mmpL5 778606 c.-126C>T upstream_gene_variant 0.33
mmpL5 778612 c.-132C>A upstream_gene_variant 0.33
mmpR5 779293 p.Ala102Ser missense_variant 0.22
mmpR5 779301 p.Glu104Asp missense_variant 0.29
rplC 800807 c.-2C>G upstream_gene_variant 0.33
fbiC 1302920 c.-11G>A upstream_gene_variant 1.0
fbiC 1303536 c.606G>T synonymous_variant 0.4
Rv1258c 1406251 p.Leu364Met missense_variant 0.2
Rv1258c 1407341 c.-1C>A upstream_gene_variant 0.17
Rv1258c 1407443 c.-103C>A upstream_gene_variant 0.2
embR 1416276 p.Arg358Ser missense_variant 0.18
embR 1416453 p.Arg299Cys missense_variant 0.13
rrs 1471915 n.70C>T non_coding_transcript_exon_variant 0.33
fabG1 1673866 p.Gly143Ser missense_variant 0.4
rpsA 1834514 p.Glu325Lys missense_variant 0.67
tlyA 1917769 c.-171C>T upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103034 c.9C>A synonymous_variant 0.67
PPE35 2169109 p.Asp502Tyr missense_variant 0.4
PPE35 2169360 p.Asn418Ser missense_variant 0.29
PPE35 2169506 c.1107G>T synonymous_variant 0.22
Rv1979c 2222991 c.174G>T synonymous_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289369 c.-128C>A upstream_gene_variant 0.25
pncA 2289750 c.-509C>A upstream_gene_variant 0.25
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519160 p.Ala349Glu missense_variant 0.2
eis 2714785 p.Arg183Pro missense_variant 0.29
eis 2715194 p.Val47Leu missense_variant 0.18
folC 2746216 p.Phe461Leu missense_variant 0.17
folC 2746277 p.Asp441Gly missense_variant 1.0
pepQ 2859441 c.978C>A synonymous_variant 0.29
ribD 2987041 p.Arg68Leu missense_variant 0.4
ribD 2987111 p.Glu91Asp missense_variant 0.29
Rv2752c 3064819 p.Gly458Ala missense_variant 0.2
Rv2752c 3065733 c.459G>A synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339361 p.Asp82Tyr missense_variant 0.33
fbiD 3339372 c.255C>T synonymous_variant 0.33
Rv3083 3449514 c.1011C>A synonymous_variant 0.33
Rv3083 3449790 p.Cys429* stop_gained 0.25
Rv3083 3449862 c.1359C>A synonymous_variant 0.12
fprA 3473940 c.-67C>A upstream_gene_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474645 c.639C>A synonymous_variant 0.4
Rv3236c 3612501 p.Val206Phe missense_variant 0.5
Rv3236c 3612839 p.Ala93Glu missense_variant 0.29
fbiA 3641276 p.Pro245Gln missense_variant 0.18
fbiB 3641529 c.-6G>T upstream_gene_variant 0.25
alr 3840969 p.Thr151Met missense_variant 0.13
rpoA 3877499 p.Asp337Asn missense_variant 0.33
clpC1 4038316 p.Gly797Cys missense_variant 0.2
clpC1 4040229 p.Gly159Val missense_variant 0.22
clpC1 4040362 p.Glu115* stop_gained 0.22
clpC1 4040396 c.309C>T synonymous_variant 0.25
panD 4043895 c.387C>A synonymous_variant 0.29
panD 4044011 p.Ala91Ser missense_variant 0.67
embC 4240830 p.Pro323His missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242775 c.-458G>A upstream_gene_variant 0.15
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245214 p.Ala661Glu missense_variant 0.2
embA 4245273 p.Arg681Cys missense_variant 0.22
embB 4245662 c.-852G>T upstream_gene_variant 0.29
embB 4247251 c.738C>A synonymous_variant 0.4
embB 4247738 p.Ala409Ser missense_variant 0.15
embB 4247809 c.1296G>A synonymous_variant 0.12
embB 4248533 p.Ala674Thr missense_variant 0.25
embB 4248612 p.Arg700His missense_variant 0.18
embB 4248794 p.Ala761Ser missense_variant 0.25
aftB 4267763 c.1074C>A synonymous_variant 0.4
ethA 4326732 p.Ala248Ser missense_variant 0.17
ethR 4327660 p.Glu38* stop_gained 0.29
ethA 4328337 c.-864C>A upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407790 p.Ala138Val missense_variant 0.29
gid 4407998 p.Gly69Cys missense_variant 0.18