TB-Profiler result

Run: ERR4821901
Summary

Run ID: ERR4821901

Sample name:

Date: 01-04-2023 17:31:03

Number of reads: 477664

Percentage reads mapped: 98.84

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 0.98
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.99
lineage1.2.2.2 Indo-Oceanic NA RD239 0.99
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 5346 p.Ser36Leu missense_variant 0.5
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8233 p.Gly311Asp missense_variant 0.18
gyrA 8414 p.Asp371Glu missense_variant 0.67
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
gyrA 9803 c.2502C>T synonymous_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 0.75
ccsA 620108 p.Asp73Gly missense_variant 0.33
rpoB 760785 p.Leu327Val missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763150 p.Phe1115Ser missense_variant 0.33
rpoC 763826 p.Ala153Thr missense_variant 0.13
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 766358 p.Ile997Val missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776158 p.Asp775His missense_variant 0.2
mmpL5 778404 p.Arg26Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303803 c.873C>A synonymous_variant 0.25
Rv1258c 1406173 p.Thr390Ala missense_variant 0.25
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417449 c.-102C>T upstream_gene_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834035 c.495delC frameshift_variant 0.2
rpsA 1834853 p.Ala438Thr missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 1.0
ndh 2102380 c.663G>T synonymous_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155574 p.Thr180Ala missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2170713 c.-101A>G upstream_gene_variant 0.2
Rv1979c 2221957 p.Glu403Gly missense_variant 1.0
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
kasA 2518612 c.498C>G synonymous_variant 0.25
eis 2714468 p.Trp289Arg missense_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747118 p.Ala161Ser missense_variant 0.18
folC 2747614 c.-16G>A upstream_gene_variant 0.25
pepQ 2859755 p.Phe222Leu missense_variant 0.12
pepQ 2860239 p.Tyr60* stop_gained 0.14
ribD 2987161 p.Ala108Asp missense_variant 0.15
Rv2752c 3065516 p.Ile226Val missense_variant 0.5
Rv2752c 3066115 p.Glu26Gly missense_variant 0.29
Rv2752c 3066222 c.-32delG upstream_gene_variant 0.22
thyX 3067308 p.Ile213Asn missense_variant 0.15
thyA 3074002 p.Gly157Asp missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087601 p.Gly261Val missense_variant 1.0
fbiD 3339243 p.Met42Ile missense_variant 0.11
fbiD 3339525 c.408G>A synonymous_variant 0.29
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449748 c.1245C>T synonymous_variant 0.11
Rv3083 3449867 p.Gly455Val missense_variant 0.17
Rv3083 3449968 c.1468delC frameshift_variant 0.29
fprA 3473837 c.-169delG upstream_gene_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474208 c.206delA frameshift_variant 0.2
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474890 p.Val295Ala missense_variant 0.13
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3613109 p.Val3Ala missense_variant 0.18
fbiA 3641099 c.561delT frameshift_variant 0.2
fbiB 3641813 c.279G>A synonymous_variant 0.18
fbiB 3642496 p.Leu321His missense_variant 0.13
alr 3840859 p.Val188Ile missense_variant 0.12
rpoA 3877943 p.Phe189Leu missense_variant 0.2
clpC1 4038437 p.Lys756Asn missense_variant 0.15
clpC1 4039052 c.1652delT frameshift_variant 0.22
clpC1 4040719 c.-15A>G upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246323 p.Leu1031Met missense_variant 0.15
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269562 p.Pro91Gln missense_variant 0.29
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4326840 p.Ile212Val missense_variant 0.4
ethA 4328322 c.-850_-849insT upstream_gene_variant 0.5
whiB6 4338199 p.Asp108Val missense_variant 0.22
whiB6 4338203 p.Arg107Cys 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 4407803 c.399delT frameshift_variant 1.0
gid 4407808 p.Asp132Ala missense_variant 1.0
gid 4407848 p.Ala119Thr missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408457 c.-255A>G upstream_gene_variant 0.4