TB-Profiler result

Run: ERR4818503
Summary

Run ID: ERR4818503

Sample name:

Date: 01-04-2023 15:35:32

Number of reads: 647347

Percentage reads mapped: 99.03

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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
pncA 2288746 c.495delC frameshift_variant 0.17 pyrazinamide, pyrazinamide
gid 4407967 p.Leu79Ser 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 6025 c.786A>G synonymous_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8006 c.705C>A synonymous_variant 0.15
gyrA 8287 p.Asn329Ser missense_variant 0.17
gyrA 8431 p.Thr377Asn missense_variant 0.11
gyrA 8550 c.1252dupC frameshift_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 1.0
fgd1 490995 c.213C>G synonymous_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491756 p.Gln325Arg missense_variant 0.2
mshA 575681 p.Val112Leu missense_variant 0.15
ccsA 620685 c.796delA frameshift_variant 0.25
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761228 c.1424dupG frameshift_variant 0.18
rpoB 761467 p.Leu554Pro missense_variant 0.2
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762512 c.-858C>A upstream_gene_variant 0.22
rpoB 762640 p.Gly945Glu missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763743 p.Leu125Pro missense_variant 0.12
rpoC 764181 p.Asp271Gly missense_variant 1.0
rpoC 766031 p.Glu888Lys missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777128 c.1353A>G synonymous_variant 0.12
mmpL5 777197 c.1283dupA frameshift_variant 0.13
mmpR5 778994 p.Ser2Ile missense_variant 0.14
mmpR5 779483 p.Asp165Gly missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302933 c.3G>A synonymous_variant 0.22
fbiC 1303708 c.778T>C synonymous_variant 0.12
fbiC 1303829 p.His300Pro missense_variant 0.12
fbiC 1304973 c.2045delA frameshift_variant 0.22
Rv1258c 1406580 p.His254Leu missense_variant 0.18
embR 1416713 p.Ile212Thr missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674754 p.Arg185Ser missense_variant 0.22
rpsA 1833897 p.Leu119Pro missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170769 c.-157C>T upstream_gene_variant 1.0
Rv1979c 2222420 p.Asp249Asn missense_variant 0.11
Rv1979c 2222462 p.Phe235Leu missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714517 c.815delA frameshift_variant 0.4
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746275 p.Val442Leu missense_variant 0.11
folC 2746800 p.Arg267Trp missense_variant 0.15
folC 2747320 c.279C>T synonymous_variant 0.4
ribD 2987529 p.Pro231Ala missense_variant 0.25
Rv2752c 3065806 p.Arg129His missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448403 c.-101G>A upstream_gene_variant 0.12
Rv3083 3448435 c.-69G>T upstream_gene_variant 0.11
Rv3083 3448682 p.Phe60Tyr missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474905 c.901_902delCG frameshift_variant 0.17
Rv3236c 3612027 p.Ile364Phe missense_variant 0.22
Rv3236c 3612385 c.732G>A synonymous_variant 0.12
fbiB 3642387 p.Thr285Ala missense_variant 0.12
clpC1 4038773 p.Asp644Glu missense_variant 0.5
clpC1 4039140 p.Glu522Gly missense_variant 0.18
panD 4044340 c.-59G>A upstream_gene_variant 0.12
embC 4239685 c.-178G>A upstream_gene_variant 1.0
embC 4241041 c.1179C>T synonymous_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242834 p.Phe991Tyr missense_variant 0.15
embA 4243135 c.-98G>A upstream_gene_variant 0.5
embA 4245505 p.Phe758Tyr missense_variant 0.22
embA 4246406 p.Glu1058Asp missense_variant 0.18
embB 4248064 c.1552delT frameshift_variant 0.33
embB 4249465 c.2952G>A synonymous_variant 0.4
aftB 4267442 c.1394delT frameshift_variant 0.14
aftB 4268298 p.Gly180Val missense_variant 0.5
aftB 4268781 p.Trp19* stop_gained 0.2
ubiA 4269276 p.Phe186Leu missense_variant 0.13
ethA 4326176 p.Glu433Gly missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338710 c.-189A>G upstream_gene_variant 0.14
gid 4407588 c.615A>G synonymous_variant 1.0