TB-Profiler result

Run: SRR5535693
Summary

Run ID: SRR5535693

Sample name:

Date: 04-04-2023 10:38:16

Number of reads: 2399285

Percentage reads mapped: 99.32

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8062 c.762delC frameshift_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491445 c.663C>A synonymous_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620786 p.Gly299Val missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763080 p.Gly1092Cys missense_variant 0.12
rpoC 763512 p.Cys48Phe missense_variant 0.13
rpoC 764456 p.Pro363Thr missense_variant 0.17
rpoC 766923 p.Glu1185Ala missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776795 c.1686C>A synonymous_variant 0.17
mmpL5 777242 c.1239C>T synonymous_variant 0.2
mmpS5 779615 c.-710C>G upstream_gene_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800644 c.-165G>T upstream_gene_variant 0.15
fbiC 1303678 c.748C>A synonymous_variant 0.2
fbiC 1305030 c.2100G>T synonymous_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472600 n.755C>A non_coding_transcript_exon_variant 0.5
rrl 1473560 n.-98G>T upstream_gene_variant 0.17
rrl 1473582 n.-76T>C upstream_gene_variant 0.14
rrl 1475102 n.1445C>A non_coding_transcript_exon_variant 0.18
rrl 1476599 n.2942C>A non_coding_transcript_exon_variant 0.33
fabG1 1673381 c.-59G>T upstream_gene_variant 0.14
fabG1 1673615 p.Glu59Gly missense_variant 0.11
inhA 1674331 p.Leu44Met missense_variant 0.14
rpsA 1833450 c.-92G>A upstream_gene_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101998 p.Ala349Ser missense_variant 0.13
ndh 2102544 p.Arg167Trp missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156326 c.-215C>A upstream_gene_variant 0.15
katG 2156342 c.-231G>T upstream_gene_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170459 p.Leu52Met missense_variant 0.12
Rv1979c 2222424 c.741G>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290124 c.-883C>A upstream_gene_variant 0.21
pncA 2290204 c.-963G>A upstream_gene_variant 0.12
kasA 2519143 c.1029G>C synonymous_variant 0.11
ribD 2987093 c.255G>T synonymous_variant 0.15
Rv2752c 3064553 p.Arg547Cys missense_variant 0.2
thyA 3074042 p.Pro144Thr missense_variant 0.2
thyA 3074124 c.348G>T synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086936 c.117C>A synonymous_variant 0.23
ald 3087446 c.627C>A synonymous_variant 0.13
ald 3087897 p.Gly360Trp missense_variant 0.17
Rv3083 3448355 c.-149C>A upstream_gene_variant 0.25
Rv3083 3448670 p.Asp56Gly missense_variant 0.17
Rv3083 3449044 p.Val181Phe missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474982 p.Gly326Trp missense_variant 0.14
Rv3236c 3612077 p.Ser347* stop_gained 0.15
Rv3236c 3612341 p.Ala259Glu missense_variant 0.14
Rv3236c 3612582 p.Leu179Ile missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612868 c.249C>A synonymous_variant 0.25
rpoA 3878211 p.Lys99Asn missense_variant 0.14
clpC1 4038795 p.Ser637Ile missense_variant 0.14
clpC1 4040665 p.Val14Phe missense_variant 0.14
embC 4241698 c.1836G>T synonymous_variant 0.14
embC 4241721 p.Thr620Asn missense_variant 0.15
embC 4241972 p.Val704Phe missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243203 c.-30C>A upstream_gene_variant 0.13
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4245563 c.-951G>T upstream_gene_variant 0.18
embB 4246253 c.-261C>A upstream_gene_variant 0.25
embB 4248452 p.Trp647Arg missense_variant 0.18
embB 4248462 p.Ser650Tyr missense_variant 0.17
embB 4249294 p.Lys927Asn missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267948 p.Asp297Tyr missense_variant 0.14
aftB 4268654 c.183A>G synonymous_variant 0.2
ethA 4326263 p.Arg404His missense_variant 0.14
ethA 4326676 p.Ser266Arg missense_variant 1.0
ethR 4328055 p.His169Gln missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0