TB-Profiler result

Run: SRR21277772

Summary

Run ID: SRR21277772

Sample name:

Date: 04-04-2023 01:40:51

Number of reads: 14173928

Percentage reads mapped: 97.37

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576253 c.906G>T synonymous_variant 0.12
mshA 576302 c.955C>T synonymous_variant 0.11
mshA 576442 p.Cys365* stop_gained 0.17
ccsA 619977 c.87G>A synonymous_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoB 761679 p.Glu625* stop_gained 0.17
rpoB 762657 p.Ala951Thr missense_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766055 p.Gly896Cys missense_variant 1.0
rpoC 766495 c.3126C>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
rplC 801252 c.444G>T synonymous_variant 0.11
fbiC 1303102 p.Leu58Met missense_variant 0.19
Rv1258c 1406760 c.580_581insC frameshift_variant 0.99
embR 1416964 c.384C>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674822 c.621C>A synonymous_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834870 c.1329C>A synonymous_variant 0.22
rpsA 1834910 p.Glu457* stop_gained 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918316 p.Pro126His missense_variant 0.19
ndh 2102225 p.Cys273Tyr missense_variant 0.12
ndh 2102348 p.Ala232Val missense_variant 0.11
ndh 2102351 p.Arg231Leu missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170348 p.Gln89* stop_gained 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519165 p.Gly351Cys missense_variant 0.18
kasA 2519179 c.1065G>T synonymous_variant 0.11
eis 2714999 p.Gly112Ser missense_variant 0.18
eis 2715565 c.-233C>T upstream_gene_variant 0.14
folC 2746299 p.Glu434* stop_gained 0.11
folC 2746313 p.Arg429Leu missense_variant 0.15
folC 2746374 p.Pro409Thr missense_variant 0.1
folC 2746527 p.Gly358Trp missense_variant 0.12
folC 2746636 c.963C>A synonymous_variant 0.12
folC 2747103 p.Ala166Thr missense_variant 0.12
folC 2747723 c.-125G>C upstream_gene_variant 0.18
pepQ 2859603 c.816G>T synonymous_variant 0.33
pepQ 2859618 c.801T>A synonymous_variant 0.22
pepQ 2859829 p.Gly197Val missense_variant 0.14
pepQ 2859957 c.462G>A synonymous_variant 0.12
pepQ 2860589 c.-171G>T upstream_gene_variant 0.18
ribD 2987485 p.Ala216Asp missense_variant 0.12
ribD 2987512 p.Arg225Leu missense_variant 0.15
Rv2752c 3066286 c.-95C>T upstream_gene_variant 0.1
Rv2752c 3067037 c.-846G>A upstream_gene_variant 0.12
Rv2752c 3067191 c.-1000G>T upstream_gene_variant 0.14
thyX 3067193 c.751_753delTGAinsCGT stop_lost&splice_region_variant 0.12
thyX 3067274 c.672C>A synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339039 c.-79G>A upstream_gene_variant 0.18
fbiD 3339052 c.-66G>T upstream_gene_variant 0.13
fbiD 3339239 p.Ala41Asp missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475301 p.Ala432Asp missense_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641439 c.-96C>T upstream_gene_variant 0.12
fbiB 3641897 c.363G>A synonymous_variant 0.14
fbiB 3642149 c.615C>A synonymous_variant 0.25
alr 3840962 c.459G>T synonymous_variant 0.1
alr 3840990 p.Ala144Val missense_variant 0.22
alr 3841204 p.Gly73Ser missense_variant 0.1
alr 3841220 c.201C>A synonymous_variant 0.13
rpoA 3878621 c.-114C>A upstream_gene_variant 0.11
clpC1 4040252 c.453C>T synonymous_variant 0.11
embC 4240410 p.Pro183Gln missense_variant 0.12
embC 4241143 c.1281C>T synonymous_variant 1.0
embC 4242369 p.Arg836His missense_variant 0.17
embA 4242460 c.-773G>A upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242761 p.Arg967Trp missense_variant 0.2
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243471 p.Ala80Asp missense_variant 0.11
embA 4243868 c.636G>A synonymous_variant 0.2
embA 4243966 p.Arg245Leu missense_variant 0.19
embA 4245460 p.Pro743His missense_variant 0.15
embA 4245488 c.2256G>T synonymous_variant 0.1
embA 4245495 p.Gly755Cys missense_variant 0.11
embA 4245685 p.Pro818Gln missense_variant 0.12
embB 4246797 p.Gly95Val missense_variant 0.29
embB 4246801 c.288G>T synonymous_variant 0.18
embB 4247620 c.1107G>A synonymous_variant 0.12
embB 4247802 p.Pro430Gln missense_variant 0.1
embB 4247812 c.1299G>T synonymous_variant 0.11
embB 4247915 p.Arg468Cys missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268321 c.516C>A synonymous_variant 0.11
aftB 4268506 c.331C>A synonymous_variant 0.13
aftB 4268543 c.294C>A synonymous_variant 0.12
aftB 4268888 c.-52C>A upstream_gene_variant 0.1
aftB 4269741 c.-905G>A upstream_gene_variant 0.12
ubiA 4270005 c.-172C>A upstream_gene_variant 0.12
ethA 4328430 c.-957A>T upstream_gene_variant 0.12
whiB6 4338575 c.-54A>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0