TB-Profiler result

Run: ERR2229711
Summary

Run ID: ERR2229711

Sample name:

Date: 31-03-2023 17:28:34

Number of reads: 579436

Percentage reads mapped: 99.19

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 6006 p.Gly256Val missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576720 p.Glu458Val missense_variant 0.25
ccsA 620254 p.Leu122Val missense_variant 0.22
rpoB 760566 p.Ser254Pro missense_variant 0.18
rpoC 763701 p.Pro111Leu missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775948 p.Ala845Thr missense_variant 0.17
mmpL5 777119 p.His454Gln missense_variant 0.2
mmpL5 777122 c.1359C>T synonymous_variant 0.2
mmpL5 777128 c.1353A>G synonymous_variant 0.2
mmpS5 778905 c.1A>G start_lost 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303562 p.Met211Thr missense_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305461 p.Ala844Val missense_variant 0.22
Rv1258c 1406236 p.Pro369Ser missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.24
rpsA 1834526 p.Arg329Cys missense_variant 0.15
rpsA 1834530 p.His330Arg missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 0.2
katG 2154341 p.Ala591Thr missense_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.11
PPE35 2169902 c.711G>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.48
PPE35 2170053 p.Thr187Ser missense_variant 0.46
Rv1979c 2223221 c.-57C>T upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714344 p.Ala330Gly missense_variant 0.11
ahpC 2726029 c.-164G>C upstream_gene_variant 0.13
folC 2746276 p.Asp441Glu missense_variant 0.15
thyA 3073912 p.Met187Lys missense_variant 0.12
thyA 3073945 p.Phe176Tyr missense_variant 0.18
clpC1 4039034 c.1671C>T synonymous_variant 0.25
clpC1 4039634 p.Glu357Gly missense_variant 0.2
embC 4240864 p.Trp334Cys missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.15
embB 4246548 p.Pro12Gln missense_variant 0.4
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4246563 p.Leu17Trp missense_variant 0.25
embB 4246567 c.54G>T synonymous_variant 0.25
aftB 4268205 p.Val211Glu missense_variant 0.2
aftB 4268216 p.Trp207Cys missense_variant 0.22
ubiA 4269864 c.-31C>T upstream_gene_variant 0.18
ethR 4326970 c.-579G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408159 p.Arg15Gln missense_variant 0.13
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0