TB-Profiler result

Run: SRR18391728
Summary

Run ID: SRR18391728

Sample name:

Date: 03-04-2023 19:41:28

Number of reads: 433137

Percentage reads mapped: 98.19

Strain: La1.7.1

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
La1 M.bovis None None 1.0
La1.7 M.bovis None None 1.0
La1.7.1 M.bovis None None 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
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide
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 5752 c.513G>A synonymous_variant 1.0
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 6847 c.-455C>T upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7534 p.Ala78Asp missense_variant 0.13
gyrA 7571 c.270G>T synonymous_variant 0.14
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7618 p.Arg106Leu missense_variant 0.13
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 8796 p.Ile499Leu missense_variant 0.11
gyrA 8805 p.Asp502Tyr missense_variant 0.12
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.96
fgd1 490798 p.Leu6Ile missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575263 c.-85C>T upstream_gene_variant 0.33
mshA 575585 p.Ala80Ser missense_variant 0.12
mshA 576029 p.His228Asp missense_variant 0.1
mshA 576462 p.Ala372Glu missense_variant 0.25
ccsA 619735 c.-156G>T upstream_gene_variant 0.15
rpoB 759988 p.Ser61Phe missense_variant 0.15
rpoB 760405 p.Pro200Gln missense_variant 0.12
rpoB 760498 p.Leu231Pro missense_variant 0.14
rpoB 761397 p.Asp531Tyr missense_variant 0.13
rpoB 762332 c.2526C>A synonymous_variant 0.12
rpoB 762906 p.Lys1034Glu missense_variant 0.1
rpoB 763009 p.Trp1068Leu missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765583 c.2214G>T synonymous_variant 0.12
rpoC 766279 c.2910C>A synonymous_variant 0.12
rpoC 766593 c.3226delG frameshift_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776365 p.Glu706* stop_gained 0.22
mmpL5 776549 c.1932C>A synonymous_variant 0.12
mmpL5 776810 p.Met557Thr missense_variant 0.14
mmpL5 778956 c.-476G>C upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801100 p.Gly98Trp missense_variant 0.14
rplC 801133 p.Gly109Cys missense_variant 0.15
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304999 p.Trp690Leu missense_variant 0.14
Rv1258c 1406592 p.Tyr250Cys missense_variant 0.12
Rv1258c 1406846 c.495C>T synonymous_variant 0.13
Rv1258c 1407269 c.72C>G synonymous_variant 0.13
Rv1258c 1407399 c.-59C>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476266 n.2609G>T non_coding_transcript_exon_variant 0.13
fabG1 1673208 c.-232T>A upstream_gene_variant 0.14
inhA 1674452 p.Ala84Glu missense_variant 0.12
rpsA 1833492 c.-50G>T upstream_gene_variant 0.14
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918625 p.Pro229Gln missense_variant 0.14
ndh 2101947 p.Asp366Tyr missense_variant 0.17
ndh 2103136 c.-94C>T upstream_gene_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155041 c.1071C>T synonymous_variant 0.14
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2155844 p.Trp90Arg missense_variant 0.11
katG 2155857 c.255C>A synonymous_variant 0.12
katG 2156025 c.87C>A synonymous_variant 1.0
katG 2156125 c.-14C>A upstream_gene_variant 0.13
katG 2156341 c.-230G>C upstream_gene_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168055 p.Pro853Leu missense_variant 0.17
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2169782 c.831G>T synonymous_variant 0.13
PPE35 2170453 p.Gly54Ser missense_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289445 c.-204C>A upstream_gene_variant 0.12
pncA 2289564 c.-323C>T upstream_gene_variant 0.14
pncA 2289995 c.-754C>T upstream_gene_variant 0.17
pncA 2290017 c.-776C>A upstream_gene_variant 0.17
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518149 p.Pro12His missense_variant 0.14
kasA 2518151 p.Ser13Arg missense_variant 0.21
kasA 2518216 p.Lys34Asn missense_variant 0.2
kasA 2518787 p.Arg225Trp missense_variant 0.25
eis 2714326 p.Gly336Asp missense_variant 0.18
folC 2746616 p.Ala328Asp missense_variant 0.13
pepQ 2859459 c.960C>A synonymous_variant 0.13
pepQ 2859475 p.Thr315Lys missense_variant 0.12
pepQ 2859620 p.Gly267Cys missense_variant 0.15
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
fbiD 3339455 p.Leu113Arg missense_variant 0.17
Rv3083 3448703 p.Arg67His missense_variant 0.12
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3448854 c.351C>A synonymous_variant 0.12
Rv3083 3448909 p.Leu136Ile missense_variant 0.14
Rv3083 3449505 c.1002C>A synonymous_variant 0.14
Rv3083 3449646 c.1143C>G synonymous_variant 0.11
Rv3083 3449691 c.1188C>A synonymous_variant 0.12
Rv3083 3449812 p.Asp437Asn missense_variant 0.13
fprA 3473881 c.-126C>A upstream_gene_variant 0.17
fprA 3473949 c.-58G>A upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3474664 p.Gly220Arg missense_variant 0.14
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475322 p.Arg439His missense_variant 0.12
fprA 3475376 c.1370G>T stop_lost&splice_region_variant 0.18
whiB7 3568416 c.264G>A synonymous_variant 0.18
Rv3236c 3612172 c.945G>A synonymous_variant 0.14
Rv3236c 3612619 p.Leu166Phe missense_variant 0.12
Rv3236c 3612730 c.387C>A synonymous_variant 0.17
Rv3236c 3612745 c.372C>A synonymous_variant 0.22
Rv3236c 3613147 c.-31G>T upstream_gene_variant 0.12
fbiB 3641962 p.Thr143Asn missense_variant 0.15
fbiB 3642219 p.Ala229Ser missense_variant 0.12
fbiB 3642478 p.Asp315Ala missense_variant 1.0
rpoA 3878208 p.Gln100His missense_variant 0.13
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
ddn 3986690 c.-154C>T upstream_gene_variant 0.13
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4040287 p.Gln140* stop_gained 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241835 p.Arg658Pro missense_variant 0.11
embC 4242446 p.Ala862Ser missense_variant 0.15
embC 4242528 p.Gly889Val missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243652 c.420T>C synonymous_variant 0.12
embA 4243662 p.Asp144Asn missense_variant 0.15
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244510 p.Leu426Phe missense_variant 0.18
embA 4244859 p.Gly543Trp missense_variant 0.2
embB 4245788 c.-726C>T upstream_gene_variant 0.22
embA 4245981 p.Gly917Arg missense_variant 0.13
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247371 c.858C>A synonymous_variant 0.14
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247815 c.1302C>T synonymous_variant 0.17
embB 4248583 c.2070C>A synonymous_variant 0.17
embB 4248846 p.Gly778Val missense_variant 0.18
embB 4249006 c.2493G>T synonymous_variant 0.12
embB 4249042 c.2529G>A synonymous_variant 0.12
embB 4249240 c.2727G>C synonymous_variant 0.2
embB 4249243 c.2730G>A synonymous_variant 0.17
embB 4249418 p.Pro969Thr missense_variant 0.12
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4267910 c.927G>A synonymous_variant 0.2
aftB 4267970 c.866delT frameshift_variant 0.14
aftB 4268817 p.Trp7* stop_gained 0.2
aftB 4268864 c.-28C>T upstream_gene_variant 0.15
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327542 c.-69A>C upstream_gene_variant 0.12
ethA 4328031 c.-558C>G upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0