TB-Profiler result

Run: SRR18391679
Summary

Run ID: SRR18391679

Sample name:

Date: 03-04-2023 19:39:35

Number of reads: 413335

Percentage reads mapped: 98.22

Strain: La1.7.1

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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 6646 c.-656C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7777 p.Arg159Leu missense_variant 0.12
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 8598 p.Gln433Lys missense_variant 0.18
gyrA 8775 p.Asp492Tyr 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 1.0
fgd1 491506 p.Ala242Thr missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575531 p.Thr62Ala missense_variant 0.12
mshA 576018 p.Val224Ala missense_variant 0.29
mshA 576169 c.822C>A synonymous_variant 0.13
mshA 576454 c.1107G>C synonymous_variant 0.11
rpoB 760421 p.Trp205* stop_gained 0.11
rpoC 762671 c.-699C>T upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764503 c.1134G>T synonymous_variant 0.13
rpoC 765149 p.Gly594Trp missense_variant 0.15
rpoC 766430 p.Gly1021Cys missense_variant 0.15
rpoC 767268 p.Ala1300Asp missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777247 c.1234C>A synonymous_variant 0.33
mmpL5 778471 p.Gln4Lys missense_variant 0.13
mmpS5 778842 p.Gly22Arg missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801214 p.Gly136Cys missense_variant 0.12
fbiC 1302749 c.-182A>G upstream_gene_variant 0.15
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1406556 p.Trp262Leu missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473623 n.-35G>T upstream_gene_variant 0.33
rrl 1475008 n.1351C>T non_coding_transcript_exon_variant 0.33
rrl 1476472 n.2815A>T non_coding_transcript_exon_variant 0.5
fabG1 1673461 p.Gly8Arg missense_variant 0.12
fabG1 1673464 p.Ala9Thr missense_variant 0.12
fabG1 1673602 p.Leu55Met missense_variant 0.17
inhA 1673718 c.-484G>T upstream_gene_variant 0.2
inhA 1674657 p.Ser152Arg missense_variant 0.12
inhA 1674833 p.Ala211Asp missense_variant 0.15
rpsA 1833956 p.Ile139Val missense_variant 0.12
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917932 c.-8A>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918156 p.Ala73Thr missense_variant 0.17
ndh 2102199 p.Ala282Thr missense_variant 0.12
ndh 2102368 c.675C>G synonymous_variant 0.12
ndh 2102707 c.336C>T synonymous_variant 0.14
ndh 2103136 c.-94C>T upstream_gene_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154042 c.2070C>T synonymous_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155239 c.873T>A synonymous_variant 0.14
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167760 c.2853G>C synonymous_variant 0.17
PPE35 2167909 p.Gly902* stop_gained 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168256 p.Leu786Gln missense_variant 0.22
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2169096 p.Leu506Ser missense_variant 0.12
PPE35 2169610 p.Gly335Ser missense_variant 0.22
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 2518865 p.Glu251Lys missense_variant 0.18
kasA 2519052 p.Thr313Lys missense_variant 0.12
folC 2746673 p.Val309Ala missense_variant 0.14
pepQ 2859566 p.Gly285Ser missense_variant 0.29
ribD 2987025 p.Ala63Thr missense_variant 0.18
thyX 3067922 c.24C>A synonymous_variant 0.14
thyA 3074650 c.-179G>C upstream_gene_variant 0.15
ald 3086695 c.-125C>A upstream_gene_variant 0.13
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
ald 3087745 p.Ser309Leu missense_variant 0.12
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474020 p.Tyr5Phe missense_variant 0.12
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3474490 p.Val162Met missense_variant 0.12
fprA 3474561 c.555G>T synonymous_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612608 p.Ala170Val missense_variant 0.29
Rv3236c 3612861 p.Leu86Met missense_variant 0.17
Rv3236c 3612870 p.Ala83Thr missense_variant 0.15
Rv3236c 3612879 c.237delG frameshift_variant 0.15
fbiB 3641558 c.24C>T synonymous_variant 0.12
fbiB 3641936 c.402C>T synonymous_variant 0.12
fbiB 3642478 p.Asp315Ala missense_variant 1.0
fbiB 3642561 p.Asp343Asn missense_variant 0.2
ddn 3986735 c.-109T>C upstream_gene_variant 0.12
clpC1 4038298 p.Asp803Tyr missense_variant 0.12
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241286 p.Pro475Leu missense_variant 0.12
embC 4241642 p.Ala594Ser missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243710 p.Gly160Trp missense_variant 0.12
embA 4244095 p.Gly288Asp missense_variant 0.15
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4245682 p.Gly817Asp missense_variant 0.12
embB 4245863 c.-651C>A upstream_gene_variant 0.12
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249063 c.2550C>T synonymous_variant 0.12
aftB 4267390 p.Gln483Lys missense_variant 0.15
aftB 4267453 p.Leu462Val missense_variant 0.11
aftB 4267858 p.Ile327Val missense_variant 1.0
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
ubiA 4269884 c.-51G>T upstream_gene_variant 0.12
ubiA 4269905 c.-72G>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408276 c.-74G>T upstream_gene_variant 0.14