TB-Profiler result

Run: SRR18391703
Summary

Run ID: SRR18391703

Sample name:

Date: 03-04-2023 19:40:25

Number of reads: 470264

Percentage reads mapped: 98.09

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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_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 491419 p.Glu213* stop_gained 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575677 c.330C>A synonymous_variant 0.12
ccsA 619789 c.-102G>T upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801208 p.Gly134Arg missense_variant 0.11
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304446 c.1520_1522delCCG disruptive_inframe_deletion 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473199 n.1354C>G non_coding_transcript_exon_variant 0.15
rrl 1475075 n.1418A>C non_coding_transcript_exon_variant 0.25
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918566 c.627C>G synonymous_variant 0.14
tlyA 1918598 p.Trp220Ser missense_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 2170283 c.330G>T synonymous_variant 0.12
PPE35 2170652 c.-40C>A upstream_gene_variant 0.15
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290222 c.-981C>A upstream_gene_variant 0.18
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518295 p.Gly61Arg missense_variant 0.17
kasA 2518322 p.Ser70Gly missense_variant 0.12
eis 2714535 c.798C>T synonymous_variant 0.14
eis 2714922 p.Leu137Phe missense_variant 0.11
eis 2714988 c.345C>T synonymous_variant 0.11
eis 2714998 p.Gly112Val missense_variant 0.11
ahpC 2726669 c.477T>C synonymous_variant 0.17
folC 2746241 c.1355_1357delCCG disruptive_inframe_deletion 0.15
folC 2746301 p.Ala433Asp missense_variant 0.15
folC 2746636 c.963C>T synonymous_variant 0.17
ribD 2987518 p.Ile227Lys missense_variant 0.12
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 3339273 c.156T>G synonymous_variant 0.21
Rv3083 3448682 p.Phe60Tyr missense_variant 0.13
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474171 c.165G>T synonymous_variant 0.14
fprA 3474191 p.Ser62Leu missense_variant 0.13
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612369 p.Thr250Ala missense_variant 1.0
fbiA 3640636 p.Ser32Pro missense_variant 1.0
fbiB 3641208 c.-327C>A upstream_gene_variant 0.12
fbiB 3642478 p.Asp315Ala missense_variant 1.0
rpoA 3878579 c.-72C>A upstream_gene_variant 0.67
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240303 c.441G>T synonymous_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243972 p.Gly247Glu missense_variant 0.12
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244522 c.1290C>G synonymous_variant 0.12
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246586 p.Gly25Arg missense_variant 0.15
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267412 c.1425T>A synonymous_variant 0.13
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268030 c.807G>A synonymous_variant 0.12
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 4270014 c.-181C>T upstream_gene_variant 0.13
ethA 4326151 c.1323C>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407718 p.Ile162Thr missense_variant 0.14
gid 4407784 p.Ala140Asp missense_variant 0.13