TB-Profiler result

Run: ERR1194813
Summary

Run ID: ERR1194813

Sample name:

Date: 31-03-2023 12:34:32

Number of reads: 661780

Percentage reads mapped: 99.1

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 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
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 6078 p.Gly280Val missense_variant 0.25
gyrB 6423 p.Trp395Leu missense_variant 0.13
gyrB 6467 c.1231_1237dupGTGTCCT frameshift_variant 0.17
gyrA 6694 c.-608C>A upstream_gene_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
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 620362 p.Ala158Thr missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762928 p.Gly1041Val missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763400 p.Arg11Ser missense_variant 0.15
rpoC 764208 p.Val280Ala missense_variant 0.5
rpoC 764358 p.Leu330Arg missense_variant 0.33
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766677 p.Asp1103Gly missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776076 p.Ala802Asp missense_variant 0.29
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.27
mmpL5 777122 c.1359C>T synonymous_variant 0.27
mmpL5 777128 c.1353A>G synonymous_variant 0.27
mmpR5 778997 p.Val3Gly missense_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800740 c.-69A>C upstream_gene_variant 0.22
fbiC 1303872 p.Tyr314* stop_gained 0.15
Rv1258c 1406170 p.Gly391Arg missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416218 p.Thr377Lys missense_variant 0.18
embR 1416231 p.Asp373Asn missense_variant 0.15
atpE 1461150 c.107delT frameshift_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473396 n.-262A>T upstream_gene_variant 0.9
rpsA 1833630 p.Ile30Thr missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834961 c.1420C>A synonymous_variant 0.4
rpsA 1834966 c.1425A>G synonymous_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167760 c.2853G>A synonymous_variant 0.13
PPE35 2167763 p.Ile950Val missense_variant 0.13
PPE35 2167790 c.2823C>G synonymous_variant 0.15
PPE35 2167799 c.2814T>G synonymous_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168238 p.Pro792Gln missense_variant 0.25
PPE35 2170170 p.Val148Gly missense_variant 0.18
Rv1979c 2223260 c.-96C>A upstream_gene_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289854 c.-613T>G upstream_gene_variant 0.29
kasA 2518879 c.765A>G synonymous_variant 0.18
kasA 2518882 c.768C>A synonymous_variant 0.17
eis 2715066 c.267G>T synonymous_variant 0.15
folC 2747561 p.Ser13* stop_gained 0.33
pepQ 2860395 c.24C>T synonymous_variant 0.14
Rv2752c 3064636 p.Val519Ala missense_variant 0.33
Rv2752c 3065500 p.Gly231Val missense_variant 1.0
thyA 3074447 p.Arg9Gly missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086941 p.Glu41Gly missense_variant 0.15
ald 3087460 p.Arg214Leu missense_variant 0.25
ald 3087670 p.Asp284Val missense_variant 0.13
Rv3083 3448889 p.Arg129Leu missense_variant 0.4
Rv3083 3449278 p.Arg259Trp missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474967 p.Ser321Ala missense_variant 0.2
fprA 3475242 c.1236A>T synonymous_variant 0.13
whiB7 3568606 p.Pro25His missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4038883 p.Gly608Cys missense_variant 0.4
clpC1 4039009 p.Leu566Met missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244854 p.Val541Gly missense_variant 0.29
embA 4245607 p.Leu792Gln missense_variant 0.33
embA 4245688 p.Val819Gly missense_variant 0.4
embB 4247028 p.Leu172Gln missense_variant 0.27
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268032 p.Pro269Thr missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407560 p.Ser215Ala missense_variant 0.5
gid 4407567 c.636C>G synonymous_variant 0.29
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407652 p.Val184Gly missense_variant 0.27
gid 4407927 p.Glu92Asp missense_variant 1.0