TB-Profiler result

Run: ERR4819203
Summary

Run ID: ERR4819203

Sample name:

Date: 01-04-2023 15:58:45

Number of reads: 865113

Percentage reads mapped: 99.26

Strain: lineage1.2.2.1

Drug-resistance: RR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.99
lineage1.2.2.1 Indo-Oceanic NA RD239 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
rpoB 761142 p.Lys446Gln missense_variant 0.11 rifampicin
pncA 2288720 c.521delA frameshift_variant 0.14 pyrazinamide
pncA 2289100 p.Lys48Glu missense_variant 0.11 pyrazinamide
ethA 4326608 p.Trp289* stop_gained 0.14 ethionamide
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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 5350 c.111C>T synonymous_variant 0.13
gyrB 5479 c.240C>T synonymous_variant 0.12
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6567 p.Ala443Val missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8319 p.Ser340Cys missense_variant 0.12
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490980 p.Asn66Lys missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576300 p.Glu318Gly missense_variant 0.15
ccsA 620547 c.657C>G synonymous_variant 0.15
ccsA 620784 c.894C>A synonymous_variant 0.17
rpoB 761904 p.Pro700Thr missense_variant 0.18
rpoB 762597 c.2793_2795delTTG disruptive_inframe_deletion 0.29
rpoB 762945 p.Thr1047Ser missense_variant 0.14
rpoB 763006 p.Cys1067Phe missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763281 p.Asn1159Tyr missense_variant 0.17
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765962 c.2593T>C synonymous_variant 0.15
rpoC 765982 c.2613C>G synonymous_variant 0.15
rpoC 765988 c.2619G>C synonymous_variant 0.13
rpoC 765994 c.2625A>T synonymous_variant 0.14
rpoC 766012 c.2643C>G synonymous_variant 0.12
rpoC 766021 c.2652G>C synonymous_variant 0.13
rpoC 766025 p.Val886Ile missense_variant 0.13
rpoC 766034 p.His889Asp missense_variant 0.14
rpoC 767201 c.3835delC frameshift_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304464 p.Gly512Ser missense_variant 0.12
fbiC 1304727 c.1797A>G synonymous_variant 0.13
embR 1416450 p.Gly300Cys missense_variant 1.0
embR 1416571 c.777G>A synonymous_variant 0.14
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417368 c.-21G>A upstream_gene_variant 0.13
atpE 1461127 p.Asp28Val missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472088 n.243T>C non_coding_transcript_exon_variant 1.0
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 1.0
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 1.0
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 1.0
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 1.0
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 1.0
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 1.0
rrl 1476778 n.3121G>T non_coding_transcript_exon_variant 0.25
inhA 1673517 c.-685G>T upstream_gene_variant 0.13
fabG1 1673950 p.Leu171Val missense_variant 0.11
inhA 1674428 p.Gly76Val missense_variant 0.2
rpsA 1834915 p.Lys458Asn missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101954 p.Gln363His missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155452 c.660G>T synonymous_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168140 p.Ala825Pro missense_variant 0.11
PPE35 2168205 p.Pro803Gln missense_variant 1.0
PPE35 2169868 c.744delC frameshift_variant 0.22
PPE35 2170032 p.Gly194Val missense_variant 0.22
PPE35 2170108 p.Ala169Ser missense_variant 0.12
Rv1979c 2221943 p.Arg408Trp missense_variant 0.13
Rv1979c 2222108 p.Phe353Leu missense_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ribD 2986723 c.-115delC upstream_gene_variant 0.15
Rv2752c 3064933 p.Ile420Asn missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339341 c.227delG frameshift_variant 0.22
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474366 c.360G>A synonymous_variant 0.2
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612804 p.Ala105Thr missense_variant 1.0
fbiA 3640987 c.447_449delTTG disruptive_inframe_deletion 0.11
alr 3840381 p.Met347Lys missense_variant 0.13
clpC1 4039745 c.960C>T synonymous_variant 0.14
clpC1 4040016 p.Ala230Val missense_variant 0.25
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040679 p.Ala9Val missense_variant 0.15
panD 4044307 c.-26A>G upstream_gene_variant 1.0
embC 4239724 c.-139A>G upstream_gene_variant 0.1
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243532 c.300C>A synonymous_variant 1.0
embA 4244890 p.Ile553Asn missense_variant 0.12
embA 4244983 c.1754dupG frameshift_variant 0.14
embA 4245152 c.1920C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.91
embA 4246275 p.Ala1015Thr missense_variant 1.0
embB 4246358 c.-156C>A upstream_gene_variant 0.18
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249265 p.Pro918Ala missense_variant 0.11
aftB 4268237 p.Met200Ile missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269469 p.Pro122Gln missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408124 p.Ala27Pro missense_variant 1.0