TB-Profiler result

Run: ERR2245356
Summary

Run ID: ERR2245356

Sample name:

Date: 31-03-2023 17:39:22

Number of reads: 1613233

Percentage reads mapped: 99.29

Strain: lineage3.1.1

Drug-resistance: Other

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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
lineage3 East-African-Indian CAS RD750 0.99
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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
ethA 4326160 p.Tyr438* stop_gained 0.12 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 5481 p.Gly81Asp missense_variant 0.17
gyrB 5523 p.Thr95Asn missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8701 p.Asp467Gly missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491162 p.Glu127Val missense_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575752 c.405G>T synonymous_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.29
ccsA 619920 c.30G>T synonymous_variant 0.22
ccsA 620423 p.Val178Ala missense_variant 0.11
rpoB 759681 c.-126C>T upstream_gene_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760002 p.Glu66Lys missense_variant 0.12
rpoB 760915 p.Arg370His missense_variant 0.17
rpoB 760997 c.1191G>T synonymous_variant 0.25
rpoB 762119 c.2313C>T synonymous_variant 0.2
rpoC 762434 c.-936T>G upstream_gene_variant 0.95
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763771 p.Tyr134* stop_gained 0.17
rpoC 765589 c.2220G>A synonymous_variant 0.2
rpoC 766519 c.3150C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775856 c.2625T>G synonymous_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776609 p.Met624Ile missense_variant 0.17
mmpL5 777684 p.Leu266Pro missense_variant 0.14
mmpR5 778292 c.-698C>T upstream_gene_variant 0.12
mmpR5 779077 p.Arg30Trp missense_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460969 c.-76G>T upstream_gene_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471718 n.-128G>T upstream_gene_variant 0.18
rrs 1471898 n.53A>T non_coding_transcript_exon_variant 0.2
rrl 1473546 n.-112G>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102105 p.Gly313Ala missense_variant 0.2
ndh 2102184 c.859A>C synonymous_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167819 p.Gly932Cys missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168269 p.Gly782Cys missense_variant 0.22
PPE35 2168674 p.Asn647Asp missense_variant 0.11
PPE35 2168843 c.1770G>T synonymous_variant 0.18
PPE35 2168890 p.Ala575Ser missense_variant 0.17
PPE35 2169029 p.Asp528Glu missense_variant 0.18
PPE35 2169063 p.Met517Lys missense_variant 0.2
PPE35 2169157 p.Thr486Pro missense_variant 0.2
PPE35 2170310 c.303G>T synonymous_variant 0.12
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2222419 p.Asp249Ala missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289041 c.201G>A synonymous_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2517977 c.-138C>T upstream_gene_variant 0.12
kasA 2518717 c.603C>A synonymous_variant 0.17
eis 2714152 p.Val394Ala missense_variant 0.22
eis 2714633 p.Lys234Glu missense_variant 0.12
eis 2714883 p.His150Gln missense_variant 0.22
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746477 c.1122T>C synonymous_variant 0.15
folC 2746712 p.Glu296Val missense_variant 0.18
folC 2746792 p.Gln269His missense_variant 0.13
folC 2746996 c.603C>T synonymous_variant 0.12
ribD 2986776 c.-63C>T upstream_gene_variant 0.12
Rv2752c 3064974 c.1218T>C synonymous_variant 0.1
Rv2752c 3065541 p.Glu217Asp missense_variant 0.18
Rv2752c 3065977 p.Asp72Gly missense_variant 0.5
thyA 3074094 c.378G>T synonymous_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087232 p.Gly138Asp missense_variant 0.12
Rv3083 3448307 c.-197T>G upstream_gene_variant 0.17
Rv3083 3448378 c.-126C>A upstream_gene_variant 0.13
Rv3083 3448509 p.Asn2Lys missense_variant 0.2
Rv3083 3448588 p.Asp29Tyr missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474903 c.897C>T synonymous_variant 0.13
whiB7 3568661 p.Pro7Ser missense_variant 0.18
Rv3236c 3612295 p.Phe274Leu missense_variant 0.12
Rv3236c 3613190 c.-74A>G upstream_gene_variant 0.2
fbiB 3641361 c.-174C>T upstream_gene_variant 0.15
fbiA 3641506 p.Ala322Thr missense_variant 0.14
fbiB 3642692 c.1158C>T synonymous_variant 0.13
alr 3840243 p.Ser393Ile missense_variant 0.13
alr 3840604 p.Pro273Ser missense_variant 0.18
clpC1 4038786 p.Gln640Leu missense_variant 0.29
clpC1 4040036 c.669C>A synonymous_variant 0.17
clpC1 4040249 p.Glu152Gly missense_variant 0.18
panD 4044275 p.Arg3Trp missense_variant 0.14
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240376 c.515delT frameshift_variant 0.17
embC 4240810 p.Trp316* stop_gained 0.22
embC 4241502 p.Ser547* stop_gained 0.2
embC 4241562 p.Arg567His missense_variant 1.0
embC 4241795 p.Asn645His missense_variant 0.15
embC 4241909 p.Ala683Ser missense_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242103 p.Lys747Asn missense_variant 0.18
embC 4242164 p.Pro768Thr missense_variant 0.14
embC 4242286 p.Phe808Leu missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243259 c.27T>C synonymous_variant 0.18
embA 4244362 p.Asn377Thr missense_variant 0.2
embA 4244606 c.1374G>A synonymous_variant 0.17
embA 4244937 p.Lys569* stop_gained 0.18
embA 4245204 p.Gly658Arg missense_variant 0.17
embA 4245723 p.Gly831* stop_gained 0.13
embA 4246039 p.Ala936Asp missense_variant 0.2
embA 4246377 p.Asp1049Tyr missense_variant 0.17
embB 4247028 p.Leu172Gln missense_variant 0.18
embB 4247303 p.Gly264Ser missense_variant 0.13
embB 4249521 p.Ala1003Asp missense_variant 0.15
embB 4249659 p.Met1049Lys missense_variant 0.18
aftB 4268089 p.Trp250Arg missense_variant 0.11
aftB 4268619 p.Val73Gly missense_variant 0.21
ethA 4327563 c.-90C>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0