TB-Profiler result

Run: ERR2228985
Summary

Run ID: ERR2228985

Sample name:

Date: 31-03-2023 16:29:17

Number of reads: 867066

Percentage reads mapped: 99.24

Strain: lineage4

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
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 8864 c.1563C>A synonymous_variant 0.12
fgd1 491366 p.Thr195Lys missense_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.3
mshA 576719 p.Glu458* stop_gained 0.2
ccsA 620442 c.552G>T synonymous_variant 0.14
ccsA 620555 p.Ala222Asp missense_variant 0.17
rpoB 762236 c.2430G>T synonymous_variant 0.12
rpoC 763646 p.Gly93Ser missense_variant 0.29
rpoC 764326 c.957G>A synonymous_variant 0.2
rpoC 764532 p.Gly388Ala missense_variant 0.2
rpoC 764541 p.Val391Gly missense_variant 0.25
rpoC 764543 p.Thr392Asp missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776867 c.1614G>C synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800987 p.Arg60Leu missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304259 c.1329C>T synonymous_variant 0.18
fbiC 1304270 p.Val447Gly missense_variant 0.2
embR 1416861 p.Ala163Ser missense_variant 0.13
embR 1417450 c.-103C>T upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473264 n.1419A>T non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475022 n.1365T>C non_coding_transcript_exon_variant 0.15
rrl 1475088 n.1431A>G non_coding_transcript_exon_variant 0.22
rrl 1475139 n.1482C>A non_coding_transcript_exon_variant 0.2
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.16
fabG1 1673361 c.-79C>G upstream_gene_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.13
inhA 1674368 p.Ala56Val missense_variant 0.13
inhA 1674403 p.Glu68Lys missense_variant 0.13
rpsA 1834751 p.Leu404Val missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102188 p.Leu285Phe missense_variant 0.12
katG 2154361 p.Phe584Ser missense_variant 0.11
PPE35 2168052 p.Val854Ala missense_variant 0.18
PPE35 2168140 p.Ala825Thr missense_variant 0.12
PPE35 2168143 p.Phe824Leu missense_variant 0.12
PPE35 2168150 c.2463T>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.15
PPE35 2169272 c.1341C>G synonymous_variant 0.15
PPE35 2169278 c.1335T>C synonymous_variant 0.27
PPE35 2169281 c.1332T>G synonymous_variant 0.29
PPE35 2169287 c.1326T>C synonymous_variant 0.15
PPE35 2169602 c.1011C>A synonymous_variant 0.14
PPE35 2169902 p.Leu237Phe missense_variant 0.21
PPE35 2169910 p.Asn235Tyr missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.36
PPE35 2170053 p.Thr187Ser missense_variant 0.4
Rv1979c 2223282 c.-118G>A upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289167 c.75C>T synonymous_variant 0.22
ahpC 2726442 p.Gly84Trp missense_variant 0.12
folC 2746959 p.Gly214Trp missense_variant 0.22
pepQ 2860492 c.-74G>C upstream_gene_variant 0.11
Rv2752c 3065743 p.Thr150Asn missense_variant 0.12
Rv2752c 3066165 c.27T>A synonymous_variant 0.18
Rv2752c 3066297 c.-106G>T upstream_gene_variant 0.2
thyX 3067340 c.606G>A synonymous_variant 0.24
thyX 3067681 p.Cys89Ser missense_variant 0.17
thyA 3074311 p.Ser54* stop_gained 0.13
thyA 3074338 p.Leu45His missense_variant 0.15
ald 3087832 p.Ala338Val missense_variant 0.12
fprA 3474918 c.912C>T synonymous_variant 0.17
fprA 3475371 c.1365C>A synonymous_variant 0.22
whiB7 3568420 p.Arg87His missense_variant 0.15
whiB7 3568727 c.-48T>A upstream_gene_variant 0.12
whiB7 3568847 c.-168G>T upstream_gene_variant 0.22
Rv3236c 3612788 p.Leu110Pro missense_variant 0.18
fbiA 3640402 c.-141C>A upstream_gene_variant 0.18
fbiB 3642516 p.Ala328Ser missense_variant 0.29
alr 3840588 p.Lys278Arg missense_variant 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.18
rpoA 3878283 p.Glu75Asp missense_variant 0.12
ddn 3986767 c.-77C>A upstream_gene_variant 0.12
clpC1 4038228 p.Pro826Leu missense_variant 0.33
clpC1 4039042 p.Ser555Thr missense_variant 0.2
embC 4241663 p.Gly601Trp missense_variant 0.17
embC 4241671 c.1809T>C synonymous_variant 0.18
embC 4241841 p.Ser660* stop_gained 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244567 c.1335C>T synonymous_variant 0.14
embA 4245814 p.Pro861Leu missense_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.6
embB 4246555 c.42G>C synonymous_variant 0.6
embB 4246556 p.Ala15Pro missense_variant 0.6
embB 4246742 p.Val77Phe missense_variant 0.14
embB 4247028 p.Leu172Arg missense_variant 0.4
aftB 4267760 p.Asp359Glu missense_variant 0.22
aftB 4268451 p.Pro129Leu missense_variant 0.2
aftB 4268826 p.Val4Gly missense_variant 0.25
aftB 4268923 c.-87C>A upstream_gene_variant 0.15
ubiA 4269001 p.Ala278Glu missense_variant 0.17
ubiA 4269047 p.Ala263Thr missense_variant 0.13
ethR 4326907 c.-642C>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408402 c.-200G>A upstream_gene_variant 0.14
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0