TB-Profiler result

Run: ERR4819831
Summary

Run ID: ERR4819831

Sample name:

Date: 01-04-2023 16:19:46

Number of reads: 584022

Percentage reads mapped: 99.25

Strain:

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
lineage1.2.1.2.1 Indo-Oceanic NA RD239 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 6112 p.Met291Ile missense_variant 1.0
gyrB 6921 p.Val561Glu missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575754 p.Val136Ala missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763609 c.240C>G synonymous_variant 0.17
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777484 p.Gln333* stop_gained 0.17
mmpL5 777529 p.Ala318Thr missense_variant 0.15
mmpR5 778160 c.-830C>A upstream_gene_variant 1.0
mmpL5 778447 p.Ser12Ala missense_variant 1.0
mmpL5 778651 c.-171C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1407007 p.Leu112Met missense_variant 0.2
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417349 c.-2C>T upstream_gene_variant 0.13
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473590 n.-68A>G upstream_gene_variant 0.4
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
fabG1 1673352 c.-88C>T upstream_gene_variant 0.11
inhA 1673406 c.-796C>G upstream_gene_variant 0.12
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102095 p.Asn316Lys missense_variant 0.13
ndh 2102118 p.Leu309Met missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169815 c.798C>T synonymous_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
eis 2714413 p.Ala307Val missense_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726659 p.Arg156His missense_variant 0.13
folC 2746187 p.Ser471* stop_gained 0.25
ribD 2986916 c.78C>G synonymous_variant 0.17
ribD 2987121 p.Gly95Arg missense_variant 0.25
ribD 2987158 p.Gln107Leu missense_variant 0.22
Rv2752c 3065627 p.Ser189Thr missense_variant 0.22
thyX 3067995 c.-50A>T upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448998 c.495C>T synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3641449 p.Val303Met missense_variant 0.11
ddn 3987063 p.Ile74Val missense_variant 0.15
clpC1 4038213 p.Asp831Gly missense_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239989 c.127C>T synonymous_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4243747 p.Gly172Val missense_variant 0.2
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249619 c.3107delT frameshift_variant 0.22
aftB 4267455 c.1381delG frameshift_variant 0.25
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269733 p.Ala34Asp missense_variant 0.15
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407557 p.Ala216Thr missense_variant 0.2
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407775 c.427delG frameshift_variant 0.22
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408009 p.Val65Gly missense_variant 1.0