TB-Profiler result

Run: ERR4819855
Summary

Run ID: ERR4819855

Sample name:

Date: 01-04-2023 16:20:31

Number of reads: 433796

Percentage reads mapped: 99.41

Strain: lineage3

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
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
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 5777 p.Phe180Leu missense_variant 0.11
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 575264 c.-84C>G upstream_gene_variant 0.14
mshA 575356 c.9T>C synonymous_variant 0.33
mshA 575761 c.414C>T synonymous_variant 0.22
mshA 575777 p.Glu144Gln missense_variant 0.33
mshA 576176 c.829C>T synonymous_variant 0.29
ccsA 620748 c.858T>G synonymous_variant 0.25
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760568 c.762G>A synonymous_variant 0.18
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764029 c.660G>A synonymous_variant 0.11
rpoC 767226 p.Pro1286Leu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777279 p.Ala401Val missense_variant 0.22
mmpL5 777409 p.Ile358Phe missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801451 p.Gly215Ser missense_variant 0.15
fbiC 1303263 c.333G>A synonymous_variant 0.12
fbiC 1304655 c.1725C>T synonymous_variant 0.2
Rv1258c 1407439 c.-99G>A upstream_gene_variant 0.2
embR 1417015 c.333T>C synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834051 c.510G>A synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918298 p.Trp120Leu missense_variant 0.12
katG 2153936 p.Ala726Thr missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154861 c.1251C>T synonymous_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167969 p.Pro882Thr missense_variant 0.12
PPE35 2167998 p.Pro872Leu missense_variant 0.12
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
pncA 2290190 c.-949C>T upstream_gene_variant 0.13
eis 2714398 p.His312Arg missense_variant 0.11
eis 2715329 c.3delG frameshift_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726269 p.Val26Gly missense_variant 0.23
ahpC 2726341 p.Val50Gly missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086803 c.-17T>C upstream_gene_variant 0.13
Rv3083 3449437 p.Gly312Ser missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474953 p.Gln316Leu missense_variant 0.11
Rv3236c 3613006 p.Leu37Phe missense_variant 0.15
fbiB 3641629 p.Ala32Val missense_variant 0.13
fbiB 3641722 c.189delT frameshift_variant 0.17
alr 3840256 p.Glu389* stop_gained 0.12
ddn 3987259 p.Trp139Leu missense_variant 0.17
panD 4044011 p.Ala91Pro missense_variant 0.11
embC 4240605 p.Leu248Pro missense_variant 0.14
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242310 c.-923C>T upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242921 p.Ala1020Asp missense_variant 0.12
embA 4244383 p.Leu384Gln missense_variant 0.17
embA 4245453 p.Ala741Thr missense_variant 0.11
ubiA 4269028 p.Gly269Asp missense_variant 0.15
whiB6 4338179 p.Ser115Thr missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
Rv1258c 1405770 c.577_*310del stop_lost&conservative_inframe_deletion&splice_region_variant 1.0