TB-Profiler result

Run: ERR2245297
Summary

Run ID: ERR2245297

Sample name:

Date: 31-03-2023 17:37:58

Number of reads: 2789460

Percentage reads mapped: 98.74

Strain: lineage3.1.1

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
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
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 5076 c.-164_-163insT upstream_gene_variant 1.0
gyrA 6763 c.-539G>T upstream_gene_variant 0.19
gyrB 6765 p.Leu509Pro missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7397 c.96G>T synonymous_variant 0.14
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.95
fgd1 490776 c.-7A>C upstream_gene_variant 0.1
fgd1 490846 p.Glu22Gln missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575461 c.114T>C synonymous_variant 0.13
mshA 575478 p.Pro44Leu missense_variant 0.14
mshA 575560 p.Tyr71* stop_gained 0.11
mshA 576108 p.Ala254Gly missense_variant 0.38
ccsA 619794 c.-97C>A upstream_gene_variant 0.18
ccsA 620148 c.258G>T synonymous_variant 0.15
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760484 p.Gln226His missense_variant 0.25
rpoB 760720 c.915delC frameshift_variant 0.13
rpoB 760744 p.Lys313Arg missense_variant 0.12
rpoB 760942 p.Ile379Thr missense_variant 0.14
rpoB 761494 p.Glu563Val missense_variant 0.15
rpoB 761676 p.Met624Val missense_variant 0.12
rpoB 761885 c.2079T>G synonymous_variant 0.15
rpoB 761954 c.2148C>T synonymous_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763313 p.Glu1169Asp missense_variant 0.22
rpoC 763473 p.Asn35Ile missense_variant 0.14
rpoC 766525 c.3156G>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776506 p.Gln659Glu missense_variant 0.15
mmpL5 777017 c.1464C>T synonymous_variant 0.15
mmpR5 779296 p.Gly103Ser missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781555 c.-5G>T upstream_gene_variant 0.2
rpsL 781563 p.Pro2Ser missense_variant 0.22
rplC 801115 p.Ala103Ser missense_variant 0.2
rplC 801141 p.Tyr111* stop_gained 0.14
fbiC 1304019 p.Asp363Glu missense_variant 0.22
fbiC 1304159 p.Val410Gly missense_variant 0.2
Rv1258c 1407508 c.-168G>T upstream_gene_variant 0.14
embR 1416675 p.Leu225Val missense_variant 0.14
atpE 1460889 c.-156T>C upstream_gene_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674837 c.636C>T synonymous_variant 0.12
rpsA 1834594 c.1053C>T synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917984 c.45C>A synonymous_variant 0.2
ndh 2102126 p.Leu306Pro missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168098 p.Val839Phe missense_variant 0.15
PPE35 2169053 c.1560T>A synonymous_variant 0.22
PPE35 2169578 c.1035T>A synonymous_variant 0.23
PPE35 2170362 p.Glu84Val missense_variant 0.15
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2222276 p.Asn297Asp missense_variant 0.11
Rv1979c 2223160 p.Val2Gly missense_variant 0.33
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
pncA 2289784 c.-543C>T upstream_gene_variant 0.14
pncA 2290075 c.-834C>A upstream_gene_variant 0.14
kasA 2517966 c.-149G>A upstream_gene_variant 0.12
kasA 2518104 c.-11G>T upstream_gene_variant 0.12
kasA 2518227 p.Ala38Val missense_variant 0.17
kasA 2518485 p.Glu124Val missense_variant 0.14
kasA 2519113 p.Gln333His missense_variant 0.17
kasA 2519141 p.Leu343Met missense_variant 0.33
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726166 c.-26_-25delTG upstream_gene_variant 0.12
folC 2746345 c.1254G>T synonymous_variant 0.14
folC 2746959 p.Gly214Arg missense_variant 0.18
folC 2747212 c.387G>T synonymous_variant 0.25
pepQ 2859499 p.Gly307Asp missense_variant 0.22
pepQ 2860592 c.-174T>A upstream_gene_variant 0.27
ribD 2986849 p.Ser4Tyr missense_variant 0.15
ribD 2987336 c.498C>T synonymous_variant 0.14
Rv2752c 3064566 c.1626G>C synonymous_variant 0.25
Rv2752c 3064906 p.Val429Gly missense_variant 0.19
Rv2752c 3065359 p.Phe278Tyr missense_variant 0.14
thyX 3067390 p.Thr186Pro missense_variant 0.29
thyA 3074512 c.-41G>A upstream_gene_variant 0.17
thyA 3074518 c.-47G>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087095 p.Phe92Leu missense_variant 0.12
ald 3087527 c.712delG frameshift_variant 0.14
fbiD 3338932 c.-186A>T upstream_gene_variant 0.14
Rv3083 3448305 c.-199T>C upstream_gene_variant 0.2
Rv3083 3448889 p.Arg129Leu missense_variant 0.27
Rv3083 3448971 c.468G>T synonymous_variant 0.5
Rv3083 3448999 p.Pro166Ser missense_variant 0.29
Rv3083 3449644 p.Ala381Ser missense_variant 0.12
fprA 3473873 c.-134T>G upstream_gene_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474874 p.Gly290Cys missense_variant 0.14
fprA 3475204 p.Glu400* stop_gained 0.18
Rv3236c 3612456 c.661C>A synonymous_variant 0.3
Rv3236c 3612472 c.645C>A synonymous_variant 0.18
Rv3236c 3612606 p.Val171Phe missense_variant 0.14
fbiB 3641855 c.321C>A synonymous_variant 0.17
fbiB 3642512 c.980_981delCC frameshift_variant 0.17
rpoA 3878344 p.Arg55Leu missense_variant 0.12
ddn 3986935 p.Arg31His missense_variant 0.17
ddn 3987021 c.178C>A synonymous_variant 0.19
clpC1 4038396 c.2308delG frameshift_variant 0.12
clpC1 4039365 p.Ala447Asp missense_variant 0.12
clpC1 4040311 p.Thr132Pro missense_variant 0.18
panD 4044245 p.Ala13Thr missense_variant 0.25
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241341 c.1479C>T synonymous_variant 0.13
embC 4241562 p.Arg567His missense_variant 1.0
embC 4241665 c.1803G>C synonymous_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243447 p.Ile72Ser missense_variant 0.13
embA 4244342 c.1110C>A synonymous_variant 0.22
embA 4244980 p.Val583Gly missense_variant 0.22
embA 4245056 c.1824C>T synonymous_variant 0.29
embA 4245615 c.2385delC frameshift_variant 0.12
embA 4245745 p.Pro838Gln missense_variant 0.33
embA 4246308 p.Thr1026Pro missense_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.38
embB 4246706 p.Gly65Ser missense_variant 0.18
embB 4248342 p.Thr610Lys missense_variant 0.12
embB 4248631 c.2118G>A synonymous_variant 0.18
aftB 4268485 p.Leu118Ile missense_variant 0.12
aftB 4268619 p.Val73Gly missense_variant 0.44
aftB 4268623 p.Trp72Gly missense_variant 0.25
aftB 4268883 c.-47G>A upstream_gene_variant 0.17
ethA 4327175 p.Phe100Ser missense_variant 0.14
ethA 4328455 c.-982G>A upstream_gene_variant 0.93
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0