TB-Profiler result

Run: ERR2229643
Summary

Run ID: ERR2229643

Sample name:

Date: 31-03-2023 17:23:13

Number of reads: 770077

Percentage reads mapped: 99.29

Strain: lineage4.8

Drug-resistance: Other

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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
panD 4043931 p.Met117Ile missense_variant 0.14 pyrazinamide
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 8666 c.1365G>T synonymous_variant 0.12
fgd1 491254 p.Lys158* stop_gained 0.17
mshA 576623 p.Ala426Pro missense_variant 0.14
mshA 576661 p.Leu438Phe missense_variant 0.15
ccsA 620321 p.Pro144Gln missense_variant 0.12
rpoB 762496 p.Asp897Gly missense_variant 0.15
rpoC 766831 c.3462C>T synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777478 p.Leu335Ile missense_variant 0.14
mmpL5 777535 p.Thr316Pro missense_variant 0.12
mmpL5 779116 c.-636G>A upstream_gene_variant 0.2
mmpL5 779376 c.-896C>T upstream_gene_variant 0.11
mmpS5 779591 c.-686C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781447 c.-113A>T upstream_gene_variant 0.14
rplC 801011 p.Gly68Val missense_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
atpE 1461077 c.33C>A synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472326 n.481T>A non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475145 n.1488C>A non_coding_transcript_exon_variant 0.17
rrl 1476005 n.2348T>C non_coding_transcript_exon_variant 0.11
rrl 1476059 n.2402G>T non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.12
inhA 1673805 c.-397G>A upstream_gene_variant 0.17
inhA 1674949 p.Leu250Met missense_variant 0.12
rpsA 1833751 c.210C>T synonymous_variant 0.13
rpsA 1834353 p.Arg271Leu missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102259 p.Ser262Pro missense_variant 0.2
ndh 2102653 p.His130Glu missense_variant 0.14
katG 2155771 p.Arg114Leu missense_variant 0.17
PPE35 2168332 c.2281C>T synonymous_variant 0.22
PPE35 2168333 c.2280C>T synonymous_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168870 c.1743G>T synonymous_variant 0.14
PPE35 2168925 p.Val563Ala missense_variant 0.12
PPE35 2169695 c.918A>G synonymous_variant 0.19
PPE35 2169902 p.Leu237Phe missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.61
PPE35 2170053 p.Thr187Ser missense_variant 0.65
Rv1979c 2223083 p.Ile28Val missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289897 c.-656G>T upstream_gene_variant 0.29
kasA 2519140 c.1026G>C synonymous_variant 0.26
kasA 2519143 c.1029G>C synonymous_variant 0.28
kasA 2519155 p.Ile347Met missense_variant 0.11
kasA 2519167 c.1053T>C synonymous_variant 0.1
kasA 2519171 p.Leu353Val missense_variant 0.1
folC 2746410 p.Val397Met missense_variant 0.15
folC 2747170 c.429T>C synonymous_variant 0.17
pepQ 2859512 p.His303Asn missense_variant 0.17
pepQ 2860222 p.Ser66* stop_gained 0.17
ribD 2986796 c.-43C>T upstream_gene_variant 0.15
ribD 2987249 c.411G>A synonymous_variant 0.2
Rv2752c 3064892 p.Gly434Ser missense_variant 0.33
Rv2752c 3067166 c.-975G>T upstream_gene_variant 0.14
thyA 3073966 p.Asp169Val missense_variant 0.15
fbiD 3339125 p.Gly3Val missense_variant 0.12
fbiD 3339491 p.Leu125Pro missense_variant 0.18
fprA 3474127 p.Met41Val missense_variant 0.13
fprA 3474259 p.Gly85Ser missense_variant 0.22
fprA 3474616 p.Gln204Lys missense_variant 0.14
fprA 3474700 p.Gly232Cys missense_variant 0.13
Rv3236c 3613057 c.60G>T synonymous_variant 0.2
alr 3841612 c.-193_-192insC upstream_gene_variant 0.22
rpoA 3878554 c.-47C>A upstream_gene_variant 0.33
ddn 3986911 p.Arg23Gln missense_variant 0.12
ddn 3987016 p.Gln58Arg missense_variant 0.12
clpC1 4038782 c.1923G>C synonymous_variant 0.11
clpC1 4039508 c.1197G>C synonymous_variant 0.15
clpC1 4039682 c.1023C>T synonymous_variant 0.12
clpC1 4040087 c.618G>T synonymous_variant 0.18
clpC1 4040144 c.561G>C synonymous_variant 0.18
clpC1 4040230 p.Gly159Arg missense_variant 0.2
panD 4043901 p.Asn127Lys missense_variant 0.13
embC 4240650 p.Leu263Pro missense_variant 0.11
embC 4241104 p.Glu414Asp missense_variant 0.14
embC 4242501 p.Ala880Glu missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243247 c.15T>C synonymous_variant 0.12
embA 4244268 c.1036C>A synonymous_variant 0.12
embA 4244519 c.1287G>T synonymous_variant 0.14
embB 4246544 p.Thr11Pro missense_variant 0.21
embB 4246548 p.Pro12Gln missense_variant 0.14
embB 4246555 c.42G>C synonymous_variant 0.13
embB 4246556 p.Ala15Pro missense_variant 0.13
embB 4248478 c.1965G>T synonymous_variant 0.12
aftB 4267826 c.1011G>T synonymous_variant 0.13
ubiA 4269467 p.Asn123His missense_variant 0.12
aftB 4269471 c.-635C>G upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0