TB-Profiler result

Run: ERR2229370
Summary

Run ID: ERR2229370

Sample name:

Date: 31-03-2023 17:08:12

Number of reads: 1291217

Percentage reads mapped: 98.7

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
gyrB 6203 p.Ser322Gly missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7674 p.Ala125Ser missense_variant 0.13
mshA 575753 p.Val136Met missense_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.33
mshA 576482 p.Val379Leu missense_variant 0.18
rpoB 759948 p.Leu48Ile missense_variant 0.17
rpoB 761152 p.Leu449Gln missense_variant 0.27
rpoC 762758 c.-612G>A upstream_gene_variant 0.13
rpoC 765888 p.Phe840Tyr missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779350 p.Gly121Trp missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801198 p.His130Gln missense_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305223 p.Asp765Tyr missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473912 n.255C>T non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474664 n.1007G>A non_coding_transcript_exon_variant 0.17
rrl 1474708 n.1051C>T non_coding_transcript_exon_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
inhA 1674974 p.Ile258Asn missense_variant 0.2
rpsA 1833688 c.147C>T synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103208 c.-166G>T upstream_gene_variant 0.14
katG 2153970 p.Asp714Glu missense_variant 0.19
katG 2154917 p.Glu399* stop_gained 0.14
katG 2156485 c.-374C>A upstream_gene_variant 0.13
PPE35 2167865 c.2748G>C synonymous_variant 0.33
PPE35 2167868 c.2745A>C synonymous_variant 0.31
PPE35 2167965 p.Ala883Gly missense_variant 0.21
PPE35 2167967 c.2646A>C synonymous_variant 0.21
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.21
PPE35 2169272 c.1341C>G synonymous_variant 0.21
PPE35 2169278 c.1335T>C synonymous_variant 0.21
PPE35 2169281 c.1332T>G synonymous_variant 0.22
PPE35 2169725 c.888T>C synonymous_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.18
PPE35 2169910 p.Asn235Tyr missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.64
PPE35 2170053 p.Thr187Ser missense_variant 0.67
PPE35 2170189 p.Glu142Gln missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519140 c.1026G>C synonymous_variant 0.12
ahpC 2726571 p.Ala127Thr missense_variant 0.12
folC 2746646 p.Gln318Arg missense_variant 0.2
folC 2746928 p.Pro224Arg missense_variant 0.12
pepQ 2859698 p.Lys241Gln missense_variant 0.11
thyX 3068015 c.-70T>G upstream_gene_variant 0.12
thyA 3074514 c.-43T>C upstream_gene_variant 0.17
fbiD 3339364 p.Pro83Ala missense_variant 0.11
alr 3840410 c.1011T>C synonymous_variant 0.15
alr 3840451 p.Gly324Trp missense_variant 0.15
alr 3841612 c.-193_-192insC upstream_gene_variant 0.21
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
rpoA 3878639 c.-132C>G upstream_gene_variant 0.25
rpoA 3878664 c.-157A>G upstream_gene_variant 0.2
clpC1 4038409 p.Pro766Thr missense_variant 0.22
clpC1 4038709 p.Ser666Pro missense_variant 0.13
clpC1 4039645 p.His354Asp missense_variant 0.14
clpC1 4039730 c.975C>G synonymous_variant 0.15
clpC1 4039794 p.Ala304Asp missense_variant 0.22
clpC1 4039829 p.Leu292Ile missense_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.24
clpC1 4040282 c.423G>T synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242648 p.Leu929Arg missense_variant 0.29
embC 4243021 p.Trp1053* stop_gained 0.12
embA 4244474 c.1242G>T synonymous_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.36
embB 4246548 p.Pro12Gln missense_variant 0.56
embB 4246555 c.42G>C synonymous_variant 0.7
embB 4246556 p.Ala15Pro missense_variant 0.7
embB 4246563 p.Leu17Trp missense_variant 0.56
embB 4246567 c.54G>T synonymous_variant 0.39
embB 4247028 p.Leu172Arg missense_variant 0.17
aftB 4268766 p.Arg24Leu missense_variant 0.17
ethR 4326961 c.-588G>C upstream_gene_variant 0.14
ethR 4326964 c.-585G>A upstream_gene_variant 0.14
ethR 4326970 c.-579G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408123 p.Ala27Val missense_variant 0.13
gid 4408292 c.-90G>A upstream_gene_variant 0.13