TB-Profiler result

Run: SRR2101754
Summary

Run ID: SRR2101754

Sample name:

Date: 03-04-2023 23:53:55

Number of reads: 509280

Percentage reads mapped: 99.59

Strain: lineage2.2.1

Drug-resistance: RR-TB

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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
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
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 7837 p.Gly179Val missense_variant 0.15
gyrA 8641 p.Glu447Gly missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491752 p.Phe324Leu missense_variant 0.14
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619904 p.His5Arg missense_variant 0.12
ccsA 620170 p.Cys94Arg missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.27
rpoB 760729 p.Tyr308Cys missense_variant 0.11
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
rplC 800895 c.87C>A synonymous_variant 0.18
Rv1258c 1406420 p.Phe307Leu missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833551 p.Pro4Ser missense_variant 0.12
rpsA 1833976 c.435C>T synonymous_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102679 p.Gly122Arg missense_variant 0.11
ndh 2102765 p.Asp93Val missense_variant 0.14
ndh 2103226 c.-184C>G upstream_gene_variant 1.0
katG 2154663 c.1449C>T synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168928 p.Ser562* stop_gained 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518258 p.Asp48Glu missense_variant 0.14
eis 2715074 p.Val87Met missense_variant 0.1
folC 2747520 p.Leu27Met missense_variant 0.2
Rv2752c 3064629 c.1563C>T synonymous_variant 0.17
ald 3086739 c.-81G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449032 p.Gly177Cys missense_variant 0.12
Rv3083 3449895 c.1394_1395delAC frameshift_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568463 p.Gln73Lys missense_variant 0.14
Rv3236c 3612011 p.Leu369Pro missense_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641401 p.Cys287Arg missense_variant 0.11
fbiB 3641837 c.303G>A synonymous_variant 0.11
clpC1 4039534 p.Asn391Asp missense_variant 0.14
clpC1 4039710 p.Ile332Thr missense_variant 0.11
clpC1 4039842 p.Glu288Gly missense_variant 0.12
panD 4044182 p.Asp34His missense_variant 0.12
panD 4044309 c.-28C>A upstream_gene_variant 0.12
embC 4241889 p.Ala676Glu missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247909 c.1396T>C synonymous_variant 0.15
embB 4249223 p.Met904Val missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4269498 c.-662A>G upstream_gene_variant 0.12
ubiA 4269990 c.-157G>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 4407927 p.Glu92Asp missense_variant 1.0