TB-Profiler result

Run: SRR21677872
Summary

Run ID: SRR21677872

Sample name:

Date: 04-04-2023 02:49:10

Number of reads: 639958

Percentage reads mapped: 99.09

Strain: lineage4.8

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 8056 p.Arg252Leu missense_variant 0.13
gyrA 8745 p.Glu482Lys missense_variant 0.14
gyrA 9788 c.2487C>T synonymous_variant 0.18
fgd1 491057 p.Thr92Asn missense_variant 0.11
mshA 576621 p.Ala425Asp missense_variant 0.4
ccsA 620074 p.Gly62Trp missense_variant 0.12
rpoB 760456 p.Gly217Asp missense_variant 0.18
rpoB 761373 p.Val523Met missense_variant 0.14
rpoC 763280 c.-90C>A upstream_gene_variant 0.12
rpoC 763451 p.Val28Ile missense_variant 0.12
rpoC 764453 p.Ala362Ser missense_variant 0.14
rpoC 765980 p.Gly871Cys missense_variant 0.12
rpoC 766869 p.Ile1167Asn missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777360 p.Ala374Val missense_variant 0.14
mmpL5 778966 c.-486T>C upstream_gene_variant 0.1
mmpR5 779443 p.Asp152Tyr missense_variant 0.11
mmpR5 779462 p.Ser158Ile missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>T upstream_gene_variant 0.12
rpsL 781620 p.Thr21Ala missense_variant 0.2
rplC 801080 p.Ala91Asp missense_variant 0.14
rplC 801206 p.Arg133His missense_variant 0.11
fbiC 1305336 c.2406T>C synonymous_variant 0.12
Rv1258c 1407235 p.Gln36Lys missense_variant 0.12
embR 1416928 c.420C>T synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472174 n.329C>T non_coding_transcript_exon_variant 0.15
rrs 1472898 n.1053T>A non_coding_transcript_exon_variant 0.11
rrs 1473078 n.1233G>A non_coding_transcript_exon_variant 0.12
rrl 1473588 n.-70G>T upstream_gene_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 1.0
inhA 1674457 p.Asn86Asp missense_variant 0.12
inhA 1674588 c.387G>T synonymous_variant 0.12
rpsA 1834963 c.1422G>T synonymous_variant 0.15
tlyA 1917881 c.-59C>G upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102268 p.Val259Phe missense_variant 0.11
PPE35 2169704 c.908delG frameshift_variant 0.2
PPE35 2169980 p.Asn211Lys missense_variant 0.14
PPE35 2170266 p.Gly116Asp missense_variant 0.13
PPE35 2170271 c.342T>C synonymous_variant 0.12
PPE35 2170280 c.333C>G synonymous_variant 0.12
PPE35 2170298 c.315A>G synonymous_variant 0.12
PPE35 2170506 p.Thr36Asn missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289487 c.-246C>A upstream_gene_variant 0.11
kasA 2518198 c.84C>T synonymous_variant 0.11
kasA 2518363 c.249C>T synonymous_variant 0.12
kasA 2518613 p.Pro167Thr missense_variant 0.13
kasA 2519041 c.927C>T synonymous_variant 0.12
eis 2714797 p.Tyr179Cys missense_variant 0.1
folC 2746527 p.Gly358Arg missense_variant 0.2
folC 2746573 p.Met342Ile missense_variant 0.25
folC 2746826 c.772delC frameshift_variant 0.18
folC 2747688 c.-90G>A upstream_gene_variant 0.14
pepQ 2859465 c.954G>T synonymous_variant 0.25
pepQ 2860133 p.Gly96Ser missense_variant 0.14
ribD 2986799 c.-40G>A upstream_gene_variant 0.12
ribD 2987537 p.Gln233His missense_variant 0.15
Rv2752c 3064840 p.Gly451Val missense_variant 0.11
Rv2752c 3065563 p.Gly210Val missense_variant 0.14
Rv2752c 3066322 c.-131G>T upstream_gene_variant 0.15
thyX 3067255 p.Glu231Lys missense_variant 0.17
thyA 3073822 p.Arg217Gln missense_variant 0.13
Rv3083 3448398 c.-106G>A upstream_gene_variant 0.13
Rv3083 3448431 c.-73T>G upstream_gene_variant 0.18
fprA 3474132 p.Leu42Phe missense_variant 0.13
fprA 3474490 p.Val162Met missense_variant 0.12
fprA 3474618 c.612G>A synonymous_variant 0.11
fprA 3475105 p.Val367Leu missense_variant 0.11
fprA 3475327 c.1321C>A synonymous_variant 0.22
fbiB 3641043 c.-492C>A upstream_gene_variant 0.18
fbiB 3642136 p.Ala201Val missense_variant 0.14
rpoA 3878566 c.-59C>T upstream_gene_variant 1.0
ddn 3986780 c.-64C>A upstream_gene_variant 0.17
embC 4241693 p.Ala611Thr missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243082 c.3221_3228delATCTGAAC frameshift_variant 0.11
embC 4243092 p.Leu1077Arg missense_variant 0.11
embC 4243095 p.Gly1078Val missense_variant 0.11
embA 4243099 c.-134G>C upstream_gene_variant 0.11
embC 4243103 p.Thr1081Pro missense_variant 0.1
embA 4245204 p.Gly658Arg missense_variant 0.17
embA 4245632 p.Asn800Lys missense_variant 0.25
embA 4246260 p.Asp1010Tyr missense_variant 0.25
embA 4246282 p.Ser1017Leu missense_variant 0.2
embB 4246520 p.Gln3Lys missense_variant 0.14
embB 4246732 c.219G>T synonymous_variant 0.11
embB 4249515 p.Leu1001Pro missense_variant 0.12
embB 4249644 p.Leu1044Pro missense_variant 0.22
embB 4249695 p.Trp1061Leu missense_variant 0.12
ubiA 4269100 c.732_733delCG frameshift_variant 0.12
ubiA 4269223 p.Ala204Asp missense_variant 0.14
ubiA 4269236 p.Glu200Lys missense_variant 0.14
ubiA 4269398 p.Ala146Ser missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408369 c.-167G>A upstream_gene_variant 0.11
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0