TB-Profiler result

Run: ERR9891974

Summary

Run ID: ERR9891974

Sample name:

Date: 02-04-2023 13:25:48

Number of reads: 582501

Percentage reads mapped: 99.71

Strain: lineage4.8

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 8034 p.Lys245Glu missense_variant 0.11
gyrA 9581 c.2280C>A synonymous_variant 0.12
gyrA 9605 c.2304C>A synonymous_variant 0.13
fgd1 491522 p.Arg247Gln missense_variant 0.14
mshA 575619 p.Arg91Leu missense_variant 0.12
ccsA 619899 c.9G>T synonymous_variant 0.17
ccsA 620262 c.372C>A synonymous_variant 0.25
ccsA 620660 p.Arg257Leu missense_variant 0.17
ccsA 620748 c.858T>G synonymous_variant 0.25
rpoC 767051 p.Glu1228* stop_gained 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776319 p.Ser721Ile missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781733 c.174G>T synonymous_variant 0.12
rplC 801076 p.Asp90Tyr missense_variant 0.12
fbiC 1302778 c.-153G>T upstream_gene_variant 0.17
fbiC 1303212 c.282C>A synonymous_variant 0.22
fbiC 1303698 c.768C>A synonymous_variant 0.11
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304497 p.Pro523Thr missense_variant 0.2
Rv1258c 1406512 p.Gly277Trp missense_variant 0.12
Rv1258c 1406522 c.819G>T synonymous_variant 0.11
Rv1258c 1406833 p.Gly170Cys missense_variant 0.15
Rv1258c 1407278 c.63G>T synonymous_variant 0.15
Rv1258c 1407410 c.-70C>A upstream_gene_variant 0.29
embR 1416417 p.Gly311Trp missense_variant 0.12
embR 1416483 p.Val289Leu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 0.98
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
inhA 1674365 p.Pro55Leu missense_variant 0.13
rpsA 1834608 p.Arg356Leu missense_variant 0.15
rpsA 1834964 c.1428delA frameshift_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101688 p.Ala452Glu missense_variant 0.14
ndh 2102386 c.656delC frameshift_variant 0.1
ndh 2103196 c.-154G>A upstream_gene_variant 0.13
katG 2154046 p.Trp689Ser missense_variant 0.14
katG 2154516 c.1596G>C synonymous_variant 0.15
katG 2154551 p.Leu521Met missense_variant 0.15
katG 2154603 c.1509C>T synonymous_variant 0.86
katG 2155716 c.396T>C synonymous_variant 0.12
katG 2156147 c.-36C>A upstream_gene_variant 0.18
PPE35 2167724 c.2889G>T synonymous_variant 0.12
PPE35 2167748 c.2864delA frameshift_variant 0.12
PPE35 2168280 p.Pro778Leu missense_variant 0.14
PPE35 2170339 p.Val92Leu missense_variant 0.11
Rv1979c 2223233 c.-69G>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289705 c.-464G>T upstream_gene_variant 0.15
kasA 2518267 c.153C>A synonymous_variant 0.14
folC 2746533 c.1065delT frameshift_variant 0.14
folC 2746537 c.1061_1062insTGCGCTC frameshift_variant 0.18
folC 2746543 c.1056C>T synonymous_variant 0.18
folC 2746546 c.1045_1052delTTCATCGA frameshift_variant 0.25
folC 2746559 p.Thr347Trp missense_variant 0.2
folC 2746561 c.1038C>G synonymous_variant 0.2
folC 2746565 c.1033_1034insTCGATGAA frameshift_variant 0.2
folC 2746569 p.Ser344Gly missense_variant 0.2
folC 2746574 c.1018_1024delGAGCGCA frameshift_variant 0.13
folC 2746584 c.1014_1015insA frameshift_variant 0.12
pepQ 2859963 c.456C>A synonymous_variant 0.25
ribD 2986985 p.Leu49Phe missense_variant 0.13
Rv2752c 3065386 p.Asn269Ser missense_variant 0.12
Rv2752c 3067101 c.-910C>A upstream_gene_variant 0.22
fbiD 3339659 c.543_544delCT frameshift_variant 0.13
Rv3083 3448466 c.-38G>T upstream_gene_variant 0.17
fprA 3474506 p.Leu167Pro missense_variant 0.18
fprA 3475167 c.1163delA frameshift_variant 0.14
whiB7 3568503 c.177G>T synonymous_variant 0.17
Rv3236c 3612208 c.909G>T synonymous_variant 0.22
Rv3236c 3612391 c.726G>T synonymous_variant 0.33
Rv3236c 3612858 p.Arg87Ser missense_variant 0.12
Rv3236c 3612878 p.Thr80Asn missense_variant 0.13
fbiA 3641057 p.Trp172Leu missense_variant 0.14
fbiB 3641545 p.Pro4His missense_variant 0.15
fbiB 3642005 c.471C>T synonymous_variant 0.25
fbiB 3642221 c.687C>G synonymous_variant 0.15
fbiB 3642877 p.Lys448Arg missense_variant 0.13
ddn 3987235 p.Pro131Leu missense_variant 1.0
embC 4240633 p.Met257Ile missense_variant 0.33
embC 4241197 c.1335G>T synonymous_variant 0.14
embC 4241839 p.Trp659Cys missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242787 c.-446G>T upstream_gene_variant 0.2
embA 4243129 c.-104G>A upstream_gene_variant 0.22
embA 4245458 p.Glu742Asp missense_variant 0.1
embA 4245594 c.2364delC frameshift_variant 0.33
embB 4246274 c.-240G>C upstream_gene_variant 0.18
embA 4246431 p.Asp1067Tyr missense_variant 0.15
embB 4246821 p.Pro103His missense_variant 0.11
embB 4247199 p.Thr229Ile missense_variant 0.15
aftB 4267906 p.Val311Leu missense_variant 0.12
aftB 4268210 c.627C>T synonymous_variant 0.12
ethA 4326064 c.1410C>A synonymous_variant 0.13
ethA 4328464 c.-991C>A upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0