TB-Profiler result

Run: SRR3732592
Summary

Run ID: SRR3732592

Sample name:

Date: 04-04-2023 05:36:25

Number of reads: 1296304

Percentage reads mapped: 99.54

Strain: lineage4.3.2

Drug-resistance: Sensitive

Download CSV Download TXT Download PDF Download JSON
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 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 5112 c.-128G>T upstream_gene_variant 0.2
gyrB 5153 c.-87C>A upstream_gene_variant 0.18
gyrB 6170 p.His311Asn missense_variant 0.17
gyrB 6957 p.Trp573Leu missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7868 c.567C>A synonymous_variant 0.15
gyrA 7952 c.651C>T synonymous_variant 0.25
gyrA 8373 p.Leu358Met missense_variant 0.14
gyrA 8421 p.Val374Met missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491150 p.Pro123Leu missense_variant 0.2
mshA 575693 p.Pro116Thr missense_variant 0.12
mshA 576476 p.Leu377Met missense_variant 0.13
ccsA 620655 p.Trp255Cys missense_variant 0.14
rpoB 759750 c.-57G>T upstream_gene_variant 0.13
rpoB 759817 p.Ser4Tyr missense_variant 0.15
rpoB 760545 p.Gly247Trp missense_variant 0.18
rpoB 760957 p.Arg384Gln missense_variant 0.18
rpoB 762243 c.2437C>A synonymous_variant 0.14
rpoC 763013 c.-357C>A upstream_gene_variant 0.14
rpoC 763355 c.-15G>T upstream_gene_variant 0.15
rpoC 763510 p.Phe47Leu missense_variant 0.12
rpoC 763900 c.531G>T synonymous_variant 0.15
rpoC 764012 p.Glu215* stop_gained 0.22
rpoC 764756 p.Leu463Ile missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765384 p.Met672Thr missense_variant 0.4
rpoC 765568 p.Met733Ile missense_variant 0.15
rpoC 765766 c.2397C>A synonymous_variant 0.17
rpoC 765965 p.Arg866Ser missense_variant 0.12
rpoC 767182 c.3813G>T synonymous_variant 0.15
rpoC 767253 p.Pro1295Gln missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776368 p.Leu705Met missense_variant 0.12
mmpL5 776500 p.Gly661Trp missense_variant 0.15
mmpL5 777376 p.Glu369* stop_gained 0.15
mmpL5 777538 p.Leu315Met missense_variant 0.15
mmpL5 777756 p.Ala242Asp missense_variant 0.2
mmpL5 777974 c.507C>A synonymous_variant 0.17
mmpL5 778036 p.Val149Phe missense_variant 0.14
mmpS5 778515 p.Val131Leu missense_variant 0.14
mmpL5 778947 c.-467C>A upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781648 p.Arg30Leu missense_variant 0.14
rplC 801066 c.258G>A synonymous_variant 0.18
fbiC 1303395 p.Trp155Cys missense_variant 0.13
fbiC 1305150 c.2220C>A synonymous_variant 0.13
Rv1258c 1407154 p.Gly63Ser missense_variant 0.15
Rv1258c 1407481 c.-141G>T upstream_gene_variant 0.25
embR 1416636 p.Asp238Tyr missense_variant 0.14
embR 1416815 p.Ala178Val missense_variant 0.2
atpE 1460850 c.-195C>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472301 n.456C>A non_coding_transcript_exon_variant 0.33
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1473047 n.1202C>A non_coding_transcript_exon_variant 0.22
rrl 1473977 n.320G>T non_coding_transcript_exon_variant 0.18
rrl 1474304 n.647G>T non_coding_transcript_exon_variant 0.15
rrl 1475385 n.1728G>T non_coding_transcript_exon_variant 0.29
rrl 1476576 n.2919C>A non_coding_transcript_exon_variant 0.4
fabG1 1673269 c.-171G>T upstream_gene_variant 0.2
fabG1 1673418 c.-22G>T upstream_gene_variant 0.14
fabG1 1673728 p.Leu97Ile missense_variant 0.22
rpsA 1833399 c.-143G>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101705 c.1338C>A synonymous_variant 0.15
katG 2154997 p.Gly372Val missense_variant 0.13
katG 2155659 c.453C>A synonymous_variant 0.18
katG 2155875 c.237C>T synonymous_variant 0.15
PPE35 2169677 c.936C>A synonymous_variant 0.22
Rv1979c 2222284 p.Ala294Val missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289166 p.Ala26Ser missense_variant 0.13
pncA 2289558 c.-317C>A upstream_gene_variant 0.17
pncA 2289665 c.-424G>T upstream_gene_variant 0.22
pncA 2289686 c.-445G>T upstream_gene_variant 0.25
kasA 2518212 p.Trp33Leu missense_variant 0.17
kasA 2519140 c.1026G>C synonymous_variant 0.14
kasA 2519143 c.1029G>C synonymous_variant 0.14
kasA 2519264 p.Val384Phe missense_variant 0.13
kasA 2519270 p.Ala386Ser missense_variant 0.12
eis 2714225 p.Ala370Ser missense_variant 0.25
eis 2714363 p.Ser324Thr missense_variant 0.15
ahpC 2726656 p.Gly155Val missense_variant 0.13
folC 2746395 p.Val402Phe missense_variant 0.2
folC 2747142 p.Glu153* stop_gained 0.2
folC 2747234 p.Ala122Val missense_variant 0.15
ribD 2986773 c.-66G>T upstream_gene_variant 0.17
Rv2752c 3065195 p.Leu333Ile missense_variant 0.17
Rv2752c 3065227 c.964delG frameshift_variant 0.14
Rv2752c 3065573 p.Glu207* stop_gained 0.18
Rv2752c 3066275 c.-84G>T upstream_gene_variant 0.17
thyX 3067247 c.699C>A synonymous_variant 0.15
thyX 3067630 p.Gln106Lys missense_variant 0.14
thyX 3067847 c.99C>A synonymous_variant 0.2
thyX 3067921 p.Val9Leu missense_variant 0.2
thyX 3068156 c.-211G>T upstream_gene_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.92
fbiD 3339555 c.438C>T synonymous_variant 0.14
Rv3083 3448358 c.-146G>A upstream_gene_variant 0.29
Rv3083 3448919 p.Cys139Phe missense_variant 0.13
Rv3083 3448944 c.441G>T synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474002 c.-5C>A upstream_gene_variant 0.17
fprA 3474583 p.Glu193* stop_gained 0.14
fprA 3475039 p.Gly345Ser missense_variant 0.33
fprA 3475143 c.1137C>A synonymous_variant 0.22
fbiA 3640535 c.-8C>A upstream_gene_variant 0.13
fbiA 3640996 p.Thr152Ala missense_variant 0.14
fbiB 3642111 p.Ala193Ser missense_variant 0.14
fbiB 3642547 p.Gly338Val missense_variant 0.29
alr 3841340 c.81G>T synonymous_variant 0.14
rpoA 3877511 p.Glu333Lys missense_variant 0.2
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039227 p.Gly493Val missense_variant 0.14
clpC1 4039445 p.Asp420Glu missense_variant 0.12
clpC1 4039697 c.1008C>G synonymous_variant 0.15
clpC1 4040757 c.-53G>T upstream_gene_variant 0.15
panD 4043881 p.Pro134His missense_variant 0.14
panD 4044089 p.Gly65Cys missense_variant 0.14
panD 4044381 c.-100C>T upstream_gene_variant 0.2
embC 4241074 c.1212G>T synonymous_variant 0.17
embC 4241215 c.1353C>A synonymous_variant 0.18
embC 4241414 p.Arg518Ser missense_variant 0.13
embC 4241437 c.1575C>A synonymous_variant 0.17
embC 4242122 p.Asp754Tyr missense_variant 0.13
embC 4242214 c.2352C>A synonymous_variant 0.14
embC 4242323 p.Gly821Cys missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242976 c.-257G>T upstream_gene_variant 0.2
embA 4243040 c.-193T>C upstream_gene_variant 0.14
embA 4244596 p.Pro455Gln missense_variant 0.13
embA 4245778 p.Ala849Asp missense_variant 0.13
embB 4245941 c.-573C>T upstream_gene_variant 0.17
embA 4245948 p.Gln906Lys missense_variant 0.18
embB 4248163 c.1650G>T synonymous_variant 0.2
embB 4248526 c.2018delT frameshift_variant 0.13
embB 4249253 p.Gly914Trp missense_variant 0.12
embB 4249589 p.Asp1026Tyr missense_variant 0.15
aftB 4266973 p.Gly622Cys missense_variant 0.14
aftB 4268581 p.Leu86Met missense_variant 0.18
ubiA 4269265 p.Gly190Val missense_variant 0.14
ethR 4326994 c.-555C>A upstream_gene_variant 0.14
ethR 4327015 c.-534G>T upstream_gene_variant 0.12
ethA 4327481 c.-8G>T upstream_gene_variant 0.12
ethR 4327624 p.Glu26* stop_gained 0.2
ethR 4327706 p.Gly53Val missense_variant 0.13
ethR 4327872 p.Asn108Lys missense_variant 0.13
gid 4407712 p.Gly164Val missense_variant 0.2
gid 4408021 p.Arg61Leu missense_variant 0.15
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408343 c.-141C>A upstream_gene_variant 0.14