TB-Profiler result

Run: ERR4817010
Summary

Run ID: ERR4817010

Sample name:

Date: 01-04-2023 14:45:22

Number of reads: 1198748

Percentage reads mapped: 99.14

Strain: lineage1.2.1.2.1

Drug-resistance: HR-TB

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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 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
lineage1.2.1.2.1 Indo-Oceanic NA 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
katG 2155253 c.858delC frameshift_variant 0.12 isoniazid
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 5128 c.-112T>C upstream_gene_variant 0.1
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6826 c.-476G>A upstream_gene_variant 0.11
gyrA 7252 c.-50G>A upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9125 c.1824C>A synonymous_variant 0.13
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
rpoB 761884 p.Gly693Asp missense_variant 0.12
rpoB 762730 p.Gln975Arg missense_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776124 p.Leu786Pro missense_variant 0.18
mmpS5 778961 c.-56C>T upstream_gene_variant 0.11
mmpR5 779179 p.Ser64Gly missense_variant 0.12
mmpR5 779455 p.Arg156* stop_gained 0.13
mmpS5 779596 c.-691G>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801069 c.261C>T synonymous_variant 0.13
fbiC 1303812 c.882C>T synonymous_variant 1.0
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
embR 1416310 c.1037delC frameshift_variant 0.11
embR 1416636 c.711delC frameshift_variant 0.13
embR 1416873 p.Val159Ile missense_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460884 c.-161C>T upstream_gene_variant 0.13
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.33
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.4
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.29
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.4
rrl 1476298 n.2641C>A non_coding_transcript_exon_variant 0.4
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.4
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.4
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 0.4
rrl 1476309 n.2652G>T non_coding_transcript_exon_variant 0.4
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
rpsA 1833721 c.180A>G synonymous_variant 0.11
rpsA 1833727 c.186G>C synonymous_variant 0.11
rpsA 1833730 c.189C>T synonymous_variant 0.11
rpsA 1833732 p.Pro64Leu missense_variant 0.12
rpsA 1833736 c.195C>T synonymous_variant 0.12
rpsA 1833742 c.201A>G synonymous_variant 0.13
rpsA 1833770 p.Asn77Asp missense_variant 0.14
rpsA 1833776 p.Val79Ile missense_variant 0.12
rpsA 1834116 p.Glu192Gly missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101991 p.Leu351Pro missense_variant 0.14
ndh 2102070 p.Ala325Thr missense_variant 0.14
ndh 2102971 c.72C>T synonymous_variant 0.15
ndh 2103047 c.-6delC upstream_gene_variant 0.17
ndh 2103200 c.-158C>T upstream_gene_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167683 p.Leu977Pro missense_variant 0.4
PPE35 2167693 p.Gly974Ser missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169101 c.1512G>T synonymous_variant 0.12
PPE35 2169829 p.Ala262Thr missense_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288868 p.Val125Ala missense_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518554 p.Pro147His missense_variant 0.17
kasA 2519048 p.Gly312Ser missense_variant 1.0
ahpC 2725963 c.-230G>A upstream_gene_variant 0.11
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064689 c.1503C>A synonymous_variant 0.11
thyA 3074594 c.-123C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086893 p.Glu25Gly missense_variant 0.1
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448550 p.Gly16Asp missense_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474043 p.Pro13Ser missense_variant 0.13
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612456 p.Arg221Trp missense_variant 0.12
Rv3236c 3613270 c.-154A>G upstream_gene_variant 0.11
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
alr 3840569 c.852G>T synonymous_variant 0.11
alr 3840664 p.Pro253Thr missense_variant 0.18
alr 3840891 p.Thr177Ile missense_variant 0.18
rpoA 3878641 c.-135delG upstream_gene_variant 0.29
ddn 3986932 p.Arg30Leu missense_variant 0.25
clpC1 4038851 c.1854G>A synonymous_variant 0.11
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 4241974 c.2112C>A synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4244835 p.Leu535Met missense_variant 0.15
embA 4244856 p.Ala542Ser missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248441 p.Thr643Asn missense_variant 0.11
aftB 4267139 c.1697delT frameshift_variant 0.12
aftB 4267398 p.Pro480Arg missense_variant 0.11
ubiA 4269215 p.Arg207Cys missense_variant 0.29
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338482 p.Ala14Ser missense_variant 0.13
whiB6 4338507 c.15C>T synonymous_variant 0.14
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 4407791 p.Ala138Thr missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408164 c.39A>T synonymous_variant 0.12