TB-Profiler result

Run: SRR4035486
Summary

Run ID: SRR4035486

Sample name:

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

Number of reads: 1384528

Percentage reads mapped: 99.47

Strain: lineage2.2.1

Drug-resistance: Other

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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
tlyA 1918538 c.602delC frameshift_variant 0.15 capreomycin
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 7821 c.520C>T synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490842 c.60C>G synonymous_variant 0.1
fgd1 491705 c.925delG frameshift_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575433 p.Gly29Val missense_variant 0.13
mshA 575716 c.369C>T synonymous_variant 0.15
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576158 p.Val271Ile missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762729 p.Gln975Glu missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303158 p.His76Gln missense_variant 0.1
fbiC 1304212 p.Val428Ile missense_variant 0.4
fbiC 1305109 p.Arg727Cys missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674838 c.640delC frameshift_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917955 p.Arg6Ser missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102155 c.888G>A synonymous_variant 0.11
ndh 2102749 c.294C>T synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170058 c.555G>A synonymous_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289923 c.-682G>A upstream_gene_variant 0.12
folC 2746566 p.Ala345Thr missense_variant 0.25
folC 2746623 p.Val326Ile missense_variant 0.29
pepQ 2859709 p.Phe237Ser missense_variant 0.13
pepQ 2859881 c.537delG frameshift_variant 0.14
ribD 2987428 p.Thr197Met missense_variant 0.25
Rv2752c 3066254 c.-63G>A upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087853 p.Thr345Met missense_variant 0.25
Rv3083 3448493 c.-11A>G upstream_gene_variant 0.18
Rv3083 3448881 c.378C>T synonymous_variant 0.12
Rv3083 3449094 c.593delG frameshift_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612011 p.Leu369Pro missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 0.83
embC 4242142 c.2283dupC frameshift_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245243 p.Ala671Thr missense_variant 0.13
embA 4245787 p.Ala852Val missense_variant 0.15
embA 4246041 p.Asp937Tyr missense_variant 0.12
embB 4246118 c.-396G>A upstream_gene_variant 0.11
embB 4249378 c.2865G>A synonymous_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267858 p.Ile327Val missense_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