TB-Profiler result

Run: ERR245825
Summary

Run ID: ERR245825

Sample name:

Date: 31-03-2023 18:23:03

Number of reads: 1980954

Percentage reads mapped: 98.78

Strain: lineage1.1.3

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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8188 p.Leu296Pro missense_variant 1.0
gyrA 8445 p.Arg382Gly missense_variant 0.21
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576184 c.837A>C synonymous_variant 0.33
ccsA 619695 c.-196G>A upstream_gene_variant 1.0
ccsA 620407 p.Pro173Ala missense_variant 0.33
rpoB 762249 p.Leu815Val missense_variant 0.19
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.98
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764702 p.Lys445Gln missense_variant 0.13
rpoC 764725 p.Phe452Leu missense_variant 0.3
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 766535 p.Glu1056Gln missense_variant 0.25
rpoC 767305 p.Tyr1312* stop_gained 0.43
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777331 p.Ala384Pro missense_variant 0.38
mmpL5 777399 p.Thr361Arg missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801166 p.Gly120Ser missense_variant 1.0
fbiC 1303152 c.222C>G synonymous_variant 0.29
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417507 c.-160A>T upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.26
rrl 1474935 n.1278A>C non_coding_transcript_exon_variant 0.33
fabG1 1673449 p.Thr4Pro missense_variant 0.35
inhA 1674883 p.Ile228Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154036 p.Ser692Arg missense_variant 0.33
katG 2154615 c.1497G>C synonymous_variant 0.3
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154758 p.Glu452Lys missense_variant 0.23
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.19
PPE35 2169866 c.747G>C synonymous_variant 0.4
PPE35 2170156 p.Ala153Pro missense_variant 0.33
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222937 c.228T>C synonymous_variant 1.0
Rv1979c 2223184 c.-20T>G upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.97
kasA 2518132 c.18C>T synonymous_variant 0.95
kasA 2518144 c.29dupG frameshift_variant 0.13
kasA 2518891 c.777C>A synonymous_variant 0.18
eis 2714366 p.Val323Leu missense_variant 0.38
ahpC 2725954 c.-239C>T upstream_gene_variant 0.32
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726756 c.564C>G synonymous_variant 0.38
pepQ 2859381 c.1038C>G synonymous_variant 0.33
pepQ 2859680 p.Leu247Val missense_variant 0.31
pepQ 2860177 p.Arg81Pro missense_variant 0.33
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064741 p.Gly484Ala missense_variant 0.33
Rv2752c 3064824 p.Asp456Glu missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.95
Rv3083 3448929 p.Tyr142* stop_gained 0.15
Rv3083 3449058 p.Ser185Arg missense_variant 0.29
Rv3083 3449673 p.Tyr390* stop_gained 0.33
Rv3083 3449731 p.Leu410Val missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474897 p.Asp297Glu missense_variant 0.29
fprA 3474942 p.Glu312Asp missense_variant 0.4
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3641534 p.Ala331Gly missense_variant 0.3
fbiB 3641955 p.Gly141Arg missense_variant 0.18
fbiB 3642173 c.639G>A synonymous_variant 1.0
fbiB 3642181 p.Val216Gly missense_variant 0.21
rpoA 3877766 p.Ala248Pro missense_variant 0.32
rpoA 3878687 c.-180A>C upstream_gene_variant 0.88
ddn 3986749 c.-95C>G upstream_gene_variant 0.17
clpC1 4039932 p.Gly258Val missense_variant 0.36
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241056 c.1194C>G synonymous_variant 0.4
embC 4241429 p.Phe523Val missense_variant 1.0
embC 4241456 p.Ala532Pro missense_variant 0.7
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.18
embA 4243848 p.Val206Met missense_variant 1.0
embB 4245713 c.-801G>C upstream_gene_variant 0.29
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248725 p.Ser738Ala missense_variant 0.43
embB 4249504 p.Gln997His missense_variant 0.19
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.35
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269870 c.-37C>G upstream_gene_variant 0.25
ethA 4327672 c.-199G>A upstream_gene_variant 0.83
ethR 4327912 p.Arg122Gly missense_variant 0.25
whiB6 4338493 p.Thr10Lys missense_variant 0.31
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0