TB-Profiler result

Run: ERR4816934
Summary

Run ID: ERR4816934

Sample name:

Date: 01-04-2023 14:42:45

Number of reads: 684885

Percentage reads mapped: 99.47

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
gyrB 5882 c.645delA frameshift_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7472 c.171T>C synonymous_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491041 p.Ala87Thr missense_variant 0.14
fgd1 491722 p.Gly314Arg missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491770 p.Pro330Thr missense_variant 0.12
rpoB 759717 c.-90A>G upstream_gene_variant 0.22
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761112 p.Gln436Lys missense_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764622 p.Leu418Arg missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776027 c.2454G>T synonymous_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776875 p.Met536Val missense_variant 0.12
mmpL5 778289 p.Met64Ile missense_variant 0.17
mmpS5 779568 c.-663C>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406940 p.Arg134Leu missense_variant 0.11
embR 1416326 p.Ile341Thr missense_variant 0.12
embR 1416776 p.Ile191Thr missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474628 n.971C>A non_coding_transcript_exon_variant 1.0
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 1.0
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 1.0
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 1.0
rrl 1474640 n.983C>T non_coding_transcript_exon_variant 1.0
inhA 1674291 c.90G>A synonymous_variant 0.17
inhA 1674522 c.321G>A synonymous_variant 0.13
rpsA 1834278 p.Asp246Gly missense_variant 0.18
tlyA 1917925 c.-14delG upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102888 p.Gln52Arg missense_variant 0.12
katG 2154214 p.Val633Ala missense_variant 0.17
katG 2154372 p.Asp580Glu missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156118 c.-7G>T upstream_gene_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168708 c.1905T>C synonymous_variant 0.13
PPE35 2169292 p.Val441Phe missense_variant 0.25
Rv1979c 2223189 c.-25T>C upstream_gene_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289445 c.-205delG upstream_gene_variant 0.12
kasA 2518351 c.237C>A synonymous_variant 0.15
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726485 p.Ala98Val missense_variant 0.14
folC 2746660 c.938delT frameshift_variant 0.11
folC 2747022 p.Val193Ile missense_variant 0.17
pepQ 2860295 p.Ala42Thr missense_variant 0.12
Rv2752c 3064862 p.Val444Leu missense_variant 0.11
Rv2752c 3067132 c.-941T>C upstream_gene_variant 0.11
thyA 3073741 p.Glu244Val missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
fbiD 3339603 c.486C>T synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474981 c.979dupG frameshift_variant 0.12
fprA 3475078 p.Gly358Trp missense_variant 0.14
fbiB 3642877 p.Lys448Arg missense_variant 1.0
rpoA 3877964 c.544C>A synonymous_variant 0.2
ddn 3986864 c.21G>A synonymous_variant 0.1
embC 4240013 p.Pro51Ser missense_variant 0.11
embC 4241923 c.2061G>T synonymous_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 0.92
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243411 p.Ala60Asp missense_variant 0.1
embA 4244801 c.1571delT frameshift_variant 0.14
embA 4245520 p.Pro763Arg missense_variant 0.33
embA 4246113 p.Val961Ile missense_variant 0.13
embA 4246117 p.Pro962Leu missense_variant 0.14
embB 4248169 c.1656C>A synonymous_variant 0.11
embB 4248360 p.Pro616Gln missense_variant 0.14
aftB 4267881 p.Gly319Asp missense_variant 0.29
ethA 4326244 c.1230C>T synonymous_variant 0.15
ethA 4327689 c.-216G>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408002 c.201T>C synonymous_variant 0.15
gid 4408432 c.-230C>T upstream_gene_variant 0.17