TB-Profiler result

Run: ERR4820979
Summary

Run ID: ERR4820979

Sample name:

Date: 01-04-2023 16:59:49

Number of reads: 407020

Percentage reads mapped: 98.12

Strain: lineage3

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 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
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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 7590 p.Val97Met missense_variant 0.12
gyrA 8362 p.Arg354His missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576431 p.Ala362Pro missense_variant 0.5
ccsA 620748 c.858T>G synonymous_variant 0.25
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764676 p.Leu436Pro missense_variant 0.12
rpoC 765273 p.Val635Ala missense_variant 0.4
rpoC 766607 p.Ile1080Leu missense_variant 0.17
rpoC 766618 c.3249G>C synonymous_variant 0.15
rpoC 766625 c.3256C>T synonymous_variant 0.14
rpoC 766651 c.3282T>C synonymous_variant 0.15
rpoC 766652 p.Ser1095Thr missense_variant 0.15
rpoC 766657 c.3288A>G synonymous_variant 0.15
rpoC 766660 c.3291G>A synonymous_variant 0.15
rpoC 766661 p.Val1098Leu missense_variant 0.15
rpoC 766667 p.Ser1100Ala missense_variant 0.15
rpoC 766672 c.3303T>C synonymous_variant 0.17
rpoC 766678 c.3309C>T synonymous_variant 0.8
rpoC 766687 c.3318G>A synonymous_variant 0.2
rpoC 766690 c.3321G>C synonymous_variant 0.22
rpoC 766693 c.3324C>T synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775718 c.2763C>G synonymous_variant 0.5
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776137 p.Ser782Ala missense_variant 0.18
mmpL5 776138 c.2343C>A synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.3
fbiC 1303379 p.Arg150His missense_variant 0.29
fbiC 1303434 p.Asp168Glu missense_variant 0.38
fbiC 1303612 p.Leu228Phe missense_variant 1.0
fbiC 1305077 p.Pro716Leu missense_variant 0.18
Rv1258c 1406597 c.744G>T synonymous_variant 0.2
Rv1258c 1407102 p.Ala80Val missense_variant 1.0
embR 1416232 p.Cys372Gly missense_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834428 p.Ile296Thr missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.5
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167681 p.Ser978Ala missense_variant 0.22
PPE35 2167689 p.Asn975Thr missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.18
PPE35 2167967 c.2646A>C synonymous_variant 0.19
PPE35 2169337 p.Asp426His missense_variant 0.15
PPE35 2169341 c.1272A>T synonymous_variant 0.15
PPE35 2169344 c.1269C>T synonymous_variant 0.15
PPE35 2169573 p.Phe347Tyr missense_variant 0.12
PPE35 2169578 c.1035T>C synonymous_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.25
PPE35 2169910 p.Asn235Tyr missense_variant 0.25
PPE35 2169964 p.Leu217Val missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.67
PPE35 2170371 p.Thr81Val missense_variant 0.33
Rv1979c 2222142 c.1023A>G synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714650 p.Val228Ala missense_variant 0.18
ahpC 2726105 c.-88G>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
fbiA 3640349 c.-194A>G upstream_gene_variant 0.11
fbiA 3640365 c.-178C>G upstream_gene_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.41
ddn 3987173 c.330C>T synonymous_variant 0.18
clpC1 4038773 p.Asp644Glu missense_variant 0.14
clpC1 4038933 p.Ala591Val missense_variant 1.0
clpC1 4039487 c.1218G>A synonymous_variant 0.29
panD 4043878 p.Arg135Leu missense_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244075 c.843C>T synonymous_variant 0.2
embA 4245875 p.Lys881Asn missense_variant 0.25
embB 4247470 c.957T>C synonymous_variant 0.22
embB 4247472 p.Phe320Tyr missense_variant 0.22
embB 4249207 c.2694G>A synonymous_variant 0.22
ethA 4327815 c.-342G>C upstream_gene_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407977 p.Gly76Arg missense_variant 0.13
gid 4408430 c.-228G>A upstream_gene_variant 1.0