TB-Profiler result

Run: ERR4796257
Summary

Run ID: ERR4796257

Sample name:

Date: 01-04-2023 06:46:36

Number of reads: 2587295

Percentage reads mapped: 92.17

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766488 p.Pro1040Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.12
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.11
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.1
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.1
rrs 1473109 n.1264T>G non_coding_transcript_exon_variant 0.1
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.1
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.13
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.15
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.13
rrl 1474551 n.894G>T non_coding_transcript_exon_variant 0.11
rrl 1474557 n.900G>T non_coding_transcript_exon_variant 0.12
rrl 1474634 n.977T>G non_coding_transcript_exon_variant 0.12
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.12
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.12
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.12
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.12
rrl 1474649 n.992A>G non_coding_transcript_exon_variant 0.14
rrl 1474652 n.996delA non_coding_transcript_exon_variant 0.14
rrl 1474658 n.1001A>T non_coding_transcript_exon_variant 0.17
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.16
rrl 1474673 n.1016T>G non_coding_transcript_exon_variant 0.15
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.15
rrl 1475080 n.1423G>C non_coding_transcript_exon_variant 0.11
rrl 1475081 n.1424C>T non_coding_transcript_exon_variant 0.11
rrl 1475082 n.1425C>G non_coding_transcript_exon_variant 0.11
rrl 1475088 n.1431A>G non_coding_transcript_exon_variant 0.1
rrl 1475108 n.1451C>G non_coding_transcript_exon_variant 0.1
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.11
rrl 1475116 n.1459G>A non_coding_transcript_exon_variant 0.11
rrl 1475137 n.1480A>G non_coding_transcript_exon_variant 0.13
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.13
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.13
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.13
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.14
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.14
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.15
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.14
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726142 c.-51G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326676 p.Ser266Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0