TB-Profiler result

Run: ERR2747605
Summary

Run ID: ERR2747605

Sample name:

Date: 31-03-2023 23:28:00

Number of reads: 650157

Percentage reads mapped: 80.54

Strain: La1.8.1

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
La1.8 M.bovis None None 1.0
La1.8.1 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 6927 p.Leu563* stop_gained 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7541 c.240C>A synonymous_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7655 c.354G>C synonymous_variant 0.18
gyrA 8048 c.747C>A synonymous_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 1.0
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 490659 c.-124G>T upstream_gene_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575504 p.His53Tyr missense_variant 0.14
mshA 575961 p.Gln205Arg missense_variant 0.12
mshA 576009 p.Ala221Val missense_variant 0.13
mshA 576122 p.Leu259Ile missense_variant 0.14
rpoB 759651 c.-156A>T upstream_gene_variant 0.4
rpoB 759970 p.Phe55Tyr missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763277 c.-93A>T upstream_gene_variant 0.4
rpoC 767178 p.Ile1270Asn missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778993 p.Ser2Gly missense_variant 0.22
mmpL5 779325 c.-845G>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801040 p.Arg78Cys missense_variant 0.17
rplC 801454 p.Glu216Gln missense_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303262 p.Pro111Leu missense_variant 0.14
fbiC 1304223 c.1293G>T synonymous_variant 0.33
fbiC 1304866 p.Gly646Arg missense_variant 0.4
fbiC 1305455 p.Arg842His missense_variant 0.15
Rv1258c 1406234 c.1106delC frameshift_variant 0.29
Rv1258c 1406861 c.480C>A synonymous_variant 0.15
Rv1258c 1407310 p.Leu11Met missense_variant 0.12
atpE 1460849 c.-196G>A upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471935 n.90T>C non_coding_transcript_exon_variant 1.0
inhA 1673715 c.-487C>G upstream_gene_variant 1.0
inhA 1674834 c.633C>T synonymous_variant 0.22
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918668 c.729G>A synonymous_variant 0.18
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2169491 c.1122T>C synonymous_variant 0.38
PPE35 2170563 p.Ala17Val missense_variant 0.18
Rv1979c 2222200 p.Gly322Asp missense_variant 0.33
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222585 p.Ala194Thr missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290028 c.-787C>T upstream_gene_variant 0.22
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
Rv2752c 3066128 p.Gly22Ser missense_variant 0.25
Rv2752c 3066146 c.46T>C synonymous_variant 0.22
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 3087461 c.642G>T synonymous_variant 0.22
fbiD 3339713 p.Arg199His missense_variant 0.14
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475026 c.1020C>T synonymous_variant 0.13
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3642551 p.Gln339His missense_variant 0.12
fbiB 3642809 c.1275G>A synonymous_variant 0.22
alr 3840785 c.636C>T synonymous_variant 0.14
alr 3841204 p.Gly73Cys missense_variant 0.15
rpoA 3877941 c.567C>T synonymous_variant 0.2
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4040833 c.-129G>T upstream_gene_variant 0.15
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241254 c.1392C>T synonymous_variant 0.25
embC 4241426 c.1564C>T synonymous_variant 0.18
embC 4242642 p.Arg927His missense_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243487 p.Asn85Lys missense_variant 0.15
embA 4244041 p.Thr270Asn missense_variant 0.17
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244854 p.Val541Glu missense_variant 0.22
embA 4245280 p.Arg683His missense_variant 0.2
embA 4245373 p.Pro714Arg missense_variant 0.17
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247309 p.Arg266Cys missense_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248734 p.Arg741Trp missense_variant 1.0
embB 4249120 c.2607C>T synonymous_variant 0.22
aftB 4267167 p.Gln557Pro missense_variant 1.0
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 4269614 p.Asp74His missense_variant 0.2
ethA 4326006 c.1468T>G stop_lost&splice_region_variant 0.4
ethA 4326024 p.Pro484Ser missense_variant 1.0
ethA 4326152 p.Arg441His missense_variant 0.22
ethA 4328213 c.-740C>T upstream_gene_variant 0.15
whiB6 4338564 c.-43C>T upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408375 c.-173G>T upstream_gene_variant 0.33