TB-Profiler result

Run: ERR4816848
Summary

Run ID: ERR4816848

Sample name:

Date: 01-04-2023 14:39:41

Number of reads: 832958

Percentage reads mapped: 99.64

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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
gyrA 6442 c.-860C>T upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7652 c.351C>A synonymous_variant 0.19
gyrA 9173 c.1872G>A synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575736 p.Cys130Phe missense_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761735 c.1929C>T synonymous_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763522 c.153C>A synonymous_variant 0.11
rpoC 763752 p.Ile128Thr missense_variant 0.1
rpoC 766694 p.Gln1109Lys missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776361 p.Gln707Arg missense_variant 0.14
mmpL5 776404 p.Pro693Ala missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800684 c.-125G>A upstream_gene_variant 0.14
rplC 800689 c.-120G>C upstream_gene_variant 0.12
fbiC 1303675 p.Gly249Ser missense_variant 0.13
Rv1258c 1406852 p.Leu163Phe missense_variant 0.1
Rv1258c 1407115 p.Met76Leu missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473453 n.-205G>A upstream_gene_variant 0.11
rrl 1473695 n.38A>G non_coding_transcript_exon_variant 0.33
rrl 1474980 n.1323G>T non_coding_transcript_exon_variant 0.4
rrl 1474981 n.1324G>C non_coding_transcript_exon_variant 0.4
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.33
fabG1 1673636 p.Asp66Gly missense_variant 0.12
fabG1 1673705 p.Ala89Val missense_variant 0.18
rpsA 1833414 c.-127delT upstream_gene_variant 0.17
rpsA 1834182 p.Gly214Asp missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102681 p.Ala121Val missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169492 p.Val374Ala missense_variant 0.11
PPE35 2169633 p.Ala327Gly missense_variant 0.11
PPE35 2170589 c.24G>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2519137 c.1023T>C synonymous_variant 0.11
eis 2714291 p.Glu348Lys missense_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3066183 c.9A>G synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475125 p.Lys373Asn missense_variant 0.1
Rv3236c 3612615 c.502C>T synonymous_variant 0.12
alr 3840679 p.Phe248Leu missense_variant 0.12
alr 3841473 c.-53G>A upstream_gene_variant 1.0
rpoA 3878144 p.Gly122Ser missense_variant 0.11
clpC1 4040119 p.Glu196* stop_gained 0.11
clpC1 4040820 c.-116G>T upstream_gene_variant 0.14
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247962 c.1449G>C synonymous_variant 0.13
embB 4248560 p.Ala683Pro missense_variant 0.12
embB 4249736 p.Pro1075Ala missense_variant 0.15
ethR 4327904 p.Ala119Val missense_variant 0.11
ethA 4328318 c.-845G>A upstream_gene_variant 0.13
whiB6 4338289 p.Gly78Val missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0