TB-Profiler result

Run: SRR4037810
Summary

Run ID: SRR4037810

Sample name:

Date: 04-04-2023 07:41:13

Number of reads: 706169

Percentage reads mapped: 99.52

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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
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
gyrB 6301 c.1062G>T synonymous_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9212 c.1911G>A synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764119 c.750G>A synonymous_variant 0.12
rpoC 767253 p.Pro1295Gln missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777286 p.Ala399Ser missense_variant 0.25
mmpL5 778323 p.Leu53Gln missense_variant 0.14
mmpL5 778650 c.-170C>T upstream_gene_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779662 c.-757G>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302946 p.Gly6Cys missense_variant 0.17
fbiC 1303318 p.Asp130Asn missense_variant 0.12
fbiC 1304880 c.1950C>T synonymous_variant 0.18
Rv1258c 1406301 p.Arg347Leu missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406810 c.531C>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473012 n.1171_1174delAAGG non_coding_transcript_exon_variant 0.11
rrl 1474235 n.578G>C non_coding_transcript_exon_variant 0.22
fabG1 1673327 c.-113A>G upstream_gene_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834458 p.Pro306Leu missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156320 c.-209C>A upstream_gene_variant 0.18
katG 2156454 c.-343G>C upstream_gene_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169691 p.Gly308Cys missense_variant 0.14
Rv1979c 2222073 c.1091dupC frameshift_variant 0.15
Rv1979c 2222570 p.Ala199Thr missense_variant 0.12
Rv1979c 2222585 p.Ala194Ser missense_variant 0.11
Rv1979c 2222715 c.450C>T synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518771 c.659delA frameshift_variant 0.25
kasA 2519295 c.1183delC frameshift_variant 0.15
ahpC 2726338 p.Val49Gly missense_variant 0.25
Rv2752c 3065105 p.Val363Ile missense_variant 0.11
thyA 3073806 c.666C>G synonymous_variant 0.13
thyA 3074169 p.Trp101* stop_gained 0.12
thyA 3074519 c.-48C>A upstream_gene_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087410 c.591A>G synonymous_variant 0.14
fbiD 3338944 c.-174G>T upstream_gene_variant 0.25
fprA 3473982 c.-25C>A upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.15
fbiB 3642867 p.Leu445Met missense_variant 0.17
alr 3841351 p.Ala24Ser missense_variant 0.12
ddn 3986824 c.-20T>C upstream_gene_variant 0.11
clpC1 4038306 c.2398delG frameshift_variant 0.17
clpC1 4038584 c.2120delC frameshift_variant 0.17
embC 4242119 p.Glu753* stop_gained 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244965 p.Ala578Asp missense_variant 0.12
embB 4248631 c.2118G>T synonymous_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4326580 c.-969G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0