TB-Profiler result

Run: ERR11050200

Summary

Run ID: ERR11050200

Sample name:

Date: 02-04-2023 15:35:57

Number of reads: 551615

Percentage reads mapped: 99.2

Strain: lineage1.2.2.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 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
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 6079 c.840C>A synonymous_variant 0.12
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6508 c.-794A>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
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 491742 c.960T>C synonymous_variant 1.0
mshA 575949 p.Val201Gly missense_variant 0.3
mshA 576606 p.Ala420Gly missense_variant 1.0
mshA 576618 p.His424Pro missense_variant 0.67
mshA 576790 c.1443A>G stop_lost&splice_region_variant 0.33
ccsA 620209 p.Trp107Arg missense_variant 0.33
ccsA 620275 p.Leu129Val missense_variant 0.2
ccsA 620282 p.Arg131His missense_variant 0.22
ccsA 620544 c.654G>A synonymous_variant 0.17
rpoB 759738 c.-69G>T upstream_gene_variant 0.33
rpoB 762901 p.Asp1032Gly missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763611 p.Glu81Ala missense_variant 0.15
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764708 p.Met447Val missense_variant 1.0
rpoC 766973 p.Ala1202Pro missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777210 p.Asp424Ala missense_variant 0.29
mmpL5 777883 p.Gly200Arg missense_variant 0.2
mmpL5 777950 c.531G>A synonymous_variant 0.2
mmpR5 779356 p.Arg123Gly missense_variant 0.12
mmpS5 779634 c.-729T>C upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303155 c.225G>C synonymous_variant 0.38
fbiC 1303157 p.His76Pro missense_variant 0.27
Rv1258c 1407069 p.Leu91Arg missense_variant 0.22
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472118 n.273A>C non_coding_transcript_exon_variant 0.2
rrs 1473183 n.1338A>T non_coding_transcript_exon_variant 0.26
rrl 1475795 n.2138A>C non_coding_transcript_exon_variant 0.33
fabG1 1673553 p.Asp38Glu missense_variant 0.33
rpsA 1834857 p.Glu439Ala missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102817 p.Leu76Val missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155793 p.Trp107Gly missense_variant 0.33
katG 2156136 c.-25A>G upstream_gene_variant 0.2
katG 2156140 c.-29C>A upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168462 c.2151C>A synonymous_variant 0.25
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2168746 p.Gly623Arg missense_variant 0.17
PPE35 2169593 c.1020C>T synonymous_variant 0.17
PPE35 2170035 p.Val193Gly missense_variant 0.43
PPE35 2170037 c.576C>G synonymous_variant 0.33
Rv1979c 2222158 p.Leu336Gln missense_variant 0.15
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222637 c.523_527dupTCGGC frameshift_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289871 c.-630T>A upstream_gene_variant 0.22
pncA 2290028 c.-787C>T upstream_gene_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518570 c.456G>T synonymous_variant 0.18
kasA 2518874 p.Ala254Ser missense_variant 0.13
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746850 p.Val250Ala missense_variant 0.2
folC 2747518 c.81G>A synonymous_variant 0.17
pepQ 2859933 c.486C>G synonymous_variant 0.29
ribD 2987498 c.660C>G synonymous_variant 0.25
Rv2752c 3064889 p.Lys435Glu missense_variant 1.0
Rv2752c 3065345 p.Asp283Asn missense_variant 0.18
ald 3086722 c.-98A>G upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087869 p.Leu350Phe missense_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449609 p.Glu369Gly missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474986 p.Val327Gly missense_variant 0.33
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612107 p.Ser337Cys missense_variant 0.2
Rv3236c 3612929 p.Pro63His missense_variant 0.2
fbiA 3641282 p.Ile247Asn missense_variant 0.18
fbiB 3641418 c.-117C>T upstream_gene_variant 0.13
fbiB 3641705 p.Glu57Asp missense_variant 0.2
alr 3841014 p.Arg136His missense_variant 0.22
alr 3841546 c.-126C>A upstream_gene_variant 1.0
clpC1 4038378 p.Thr776Ile missense_variant 0.12
clpC1 4039702 p.Asp335His missense_variant 0.22
clpC1 4040235 p.Gly157Ala missense_variant 0.38
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241116 c.1254C>T synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243585 p.Phe118Ser missense_variant 0.3
embA 4244776 p.Met515Thr missense_variant 0.12
embA 4245907 p.Leu892Gln missense_variant 0.29
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246909 c.396C>T synonymous_variant 0.15
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248804 p.Met764Lys missense_variant 0.17
embB 4248935 p.Gln808* stop_gained 0.15
aftB 4268440 p.Asp133His missense_variant 0.21
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326041 p.Leu478Pro missense_variant 0.1
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4328415 c.-942A>G upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408096 p.Val36Gly missense_variant 0.33