TB-Profiler result

Run: ERR9030495

Summary

Run ID: ERR9030495

Sample name:

Date: 02-04-2023 09:27:46

Number of reads: 1671759

Percentage reads mapped: 98.94

Strain: lineage1

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
lineage1 Indo-Oceanic EAI RD239 0.97
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
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.4 streptomycin
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 0.99
gyrB 6124 c.885C>T synonymous_variant 0.99
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.94
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.98
mshA 575576 c.229C>T synonymous_variant 0.17
mshA 576632 p.Ser429Pro missense_variant 0.29
ccsA 620631 c.741T>G synonymous_variant 0.11
ccsA 620649 c.759A>G synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779427 p.Met146Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801221 p.Ser138Asn missense_variant 0.29
fbiC 1303494 c.564G>A synonymous_variant 0.94
Rv1258c 1406153 c.1188G>A synonymous_variant 0.25
Rv1258c 1407330 p.Ser4Asn missense_variant 0.12
Rv1258c 1407361 c.-21C>A upstream_gene_variant 0.14
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.67
rrl 1474960 n.1303C>G non_coding_transcript_exon_variant 0.67
rrl 1474963 n.1306G>T non_coding_transcript_exon_variant 0.67
rrl 1474964 n.1307T>A non_coding_transcript_exon_variant 0.67
rrl 1474965 n.1308G>C non_coding_transcript_exon_variant 0.67
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.5
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.6
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918025 p.Ala29Val missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155807 p.Phe102Tyr missense_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 0.94
PPE35 2167983 p.Gly877Asp missense_variant 0.96
Rv1979c 2222308 p.Asp286Gly missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715512 c.-180T>G upstream_gene_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726468 c.276G>A synonymous_variant 1.0
folC 2746226 p.Gly458Val missense_variant 0.22
folC 2746501 c.1098G>C synonymous_variant 0.17
folC 2747634 c.-36A>G upstream_gene_variant 0.12
folC 2747766 c.-168A>G upstream_gene_variant 0.17
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3066303 c.-112C>A upstream_gene_variant 0.15
Rv2752c 3067086 c.-895A>G upstream_gene_variant 0.22
thyX 3067491 p.Ala152Val missense_variant 1.0
thyX 3067927 c.19C>T synonymous_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339255 c.138G>A synonymous_variant 0.13
Rv3083 3448714 p.Asp71His missense_variant 0.94
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.95
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612041 p.Val359Ala missense_variant 1.0
Rv3236c 3612130 c.987G>A synonymous_variant 0.12
fbiB 3641570 c.36C>T synonymous_variant 0.14
alr 3840496 c.925C>T synonymous_variant 0.12
rpoA 3878463 c.45C>A synonymous_variant 0.12
rpoA 3878472 p.Asp12Glu missense_variant 0.13
rpoA 3878478 c.30C>G synonymous_variant 0.14
rpoA 3878484 c.24C>A synonymous_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 0.99
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241126 p.Leu422Met missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242685 c.-548C>T upstream_gene_variant 1.0
embC 4242906 p.Arg1015Gln missense_variant 0.12
embA 4243465 p.Ala78Asp missense_variant 0.2
embA 4243551 p.Val107Ile missense_variant 0.33
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244057 c.825C>T synonymous_variant 0.14
embA 4244450 c.1218C>T synonymous_variant 0.22
embA 4244598 p.Leu456Met missense_variant 0.33
embA 4244851 p.Arg540His missense_variant 0.25
embA 4244885 c.1653A>G synonymous_variant 0.33
embB 4245797 c.-717C>T upstream_gene_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247026 c.513G>A synonymous_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4270012 c.-179G>A upstream_gene_variant 0.2
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 4407873 c.330G>T synonymous_variant 1.0
gid 4408365 c.-163C>T upstream_gene_variant 1.0
gid 4408449 c.-247C>G upstream_gene_variant 1.0