TB-Profiler result

Run: ERR4821238

Summary

Run ID: ERR4821238

Sample name:

Date: 01-04-2023 17:08:29

Number of reads: 574477

Percentage reads mapped: 99.41

Strain: lineage3

Drug-resistance: HR-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
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4408066 c.136delG frameshift_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 5537 p.Met100Leu missense_variant 0.12
gyrA 7285 c.-17T>C upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9562 p.Met754Thr missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759934 p.Glu43Val missense_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762721 p.Asp972Gly missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764927 p.Lys520Glu missense_variant 0.15
rpoC 766207 c.2838T>C synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775705 p.Thr926Ser missense_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777062 c.1418delT frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406216 c.1125A>T synonymous_variant 0.13
atpE 1461006 c.-39C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474370 n.713C>G non_coding_transcript_exon_variant 0.67
rrl 1476446 n.2789C>T non_coding_transcript_exon_variant 0.29
fabG1 1673906 p.Ser156Phe missense_variant 0.18
inhA 1674953 p.Pro251Gln missense_variant 0.17
inhA 1674997 p.Thr266Ala missense_variant 0.1
tlyA 1917743 c.-197G>T upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102024 c.1018delG frameshift_variant 0.1
ndh 2103166 c.-124C>T upstream_gene_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156368 c.-257G>A upstream_gene_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223053 p.Glu38Lys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289326 c.-102_-86delTGGTCATGTTCGCGATC upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2290095 c.-854C>G upstream_gene_variant 0.12
kasA 2518565 p.Ala151Thr missense_variant 0.15
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyX 3067769 c.177C>A synonymous_variant 0.12
thyX 3067796 c.150C>T synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087203 c.384C>A synonymous_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474101 p.Leu32Pro missense_variant 0.15
Rv3236c 3612039 p.Phe360Ile missense_variant 0.12
fbiB 3641664 p.Asp44Asn missense_variant 0.17
fbiB 3642121 p.Asp196Val missense_variant 0.29
fbiB 3642799 c.1266delC frameshift_variant 0.29
alr 3840953 c.468C>A synonymous_variant 0.11
alr 3841473 c.-53G>A upstream_gene_variant 1.0
alr 3841524 c.-104G>A upstream_gene_variant 0.17
clpC1 4038405 p.Val767Ala missense_variant 0.2
clpC1 4038520 c.2185C>A synonymous_variant 0.14
embC 4241494 c.1632C>G synonymous_variant 0.15
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243602 p.Ala124Ser missense_variant 0.11
embA 4244930 c.1698G>A synonymous_variant 0.25
embA 4246170 p.Asp980Tyr missense_variant 0.15
embB 4246587 p.Gly25Ala missense_variant 0.13
embB 4246812 p.Gly100Asp missense_variant 0.13
embB 4247128 c.615C>T synonymous_variant 0.14
aftB 4268516 c.321A>T synonymous_variant 0.14
ethR 4327604 p.Arg19Gln missense_variant 0.25
ethA 4328455 c.-982G>A upstream_gene_variant 0.25
whiB6 4338539 c.-18G>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407696 p.Asp169Glu missense_variant 0.14
gid 4408328 c.-126G>A upstream_gene_variant 0.18