TB-Profiler result

Run: ERR1750902
Summary

Run ID: ERR1750902

Sample name:

Date: 31-03-2023 14:58:51

Number of reads: 1080660

Percentage reads mapped: 98.54

Strain: lineage2.2.1

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
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
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8921 c.1620C>A synonymous_variant 0.12
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 620625 p.Ile245Met missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.5
rpoB 760487 c.681G>A synonymous_variant 0.17
rpoB 761133 c.1327T>C synonymous_variant 0.29
rpoB 762318 p.Ser838Pro missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763271 p.Asn1155Lys missense_variant 0.22
rpoB 763290 p.Arg1162Ser missense_variant 0.22
rpoC 763448 p.Glu27Lys missense_variant 0.17
rpoC 763871 p.Gly168Cys missense_variant 0.17
rpoC 764752 c.1383G>T synonymous_variant 0.15
rpoC 765013 c.1644C>T synonymous_variant 1.0
rpoC 765330 p.Ser654Asn missense_variant 0.15
rpoC 766090 c.2721C>T synonymous_variant 0.12
rpoC 766336 c.2967C>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775853 c.2628C>A synonymous_variant 0.17
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 778188 p.Gln98Leu missense_variant 0.18
mmpL5 778304 p.Ile59Met missense_variant 0.12
mmpL5 778528 c.-48G>T upstream_gene_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781363 c.-197T>G upstream_gene_variant 0.38
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800701 c.-108G>C upstream_gene_variant 0.14
rplC 800768 c.-41C>A upstream_gene_variant 0.23
fbiC 1304393 p.Pro488Leu missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417248 c.99delC frameshift_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471837 n.-9G>A upstream_gene_variant 0.13
rrl 1473865 n.208T>A non_coding_transcript_exon_variant 0.2
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 0.2
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.18
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.18
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.18
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.18
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.18
rrl 1475208 n.1551C>A non_coding_transcript_exon_variant 0.22
fabG1 1673261 c.-179C>A upstream_gene_variant 0.14
inhA 1673584 c.-618T>C upstream_gene_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918271 p.Ala111Asp missense_variant 0.15
ndh 2102162 p.Arg294Leu missense_variant 0.14
ndh 2102285 p.Asp253Gly missense_variant 0.13
ndh 2102538 p.Lys169Gln missense_variant 0.27
ndh 2103225 c.-183A>C upstream_gene_variant 0.44
katG 2154405 c.1707G>T synonymous_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155333 p.Val260Ala missense_variant 0.11
katG 2155745 p.Gly123Arg missense_variant 0.14
katG 2156466 c.-355G>T upstream_gene_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168389 p.Gln742Lys missense_variant 0.14
PPE35 2170293 p.Pro107Gln missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288938 p.Ala102Ser missense_variant 0.12
pncA 2289251 c.-10T>A upstream_gene_variant 0.12
kasA 2518151 p.Ser13Arg missense_variant 0.25
kasA 2519137 c.1023T>C synonymous_variant 0.12
ahpC 2726269 p.Val26Gly missense_variant 0.18
ahpC 2726338 p.Val49Gly missense_variant 0.33
folC 2747071 c.527delG frameshift_variant 0.13
folC 2747428 c.171G>T synonymous_variant 0.18
thyA 3073814 p.Leu220Ile missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448530 c.27C>A synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568626 p.Leu18Phe missense_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640372 c.-171A>T upstream_gene_variant 0.17
alr 3840207 p.Ala405Asp missense_variant 0.2
panD 4043876 p.Leu136Ile missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246868 p.Ser119Gly missense_variant 0.15
embB 4246872 p.Ala120Asp missense_variant 0.15
aftB 4267099 p.Ala580Ser missense_variant 0.12
aftB 4267329 p.Arg503Gln missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267649 c.1188T>A synonymous_variant 0.18
ethA 4328406 c.-933C>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338625 c.-104C>A upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0