TB-Profiler result

Run: ERR2229190
Summary

Run ID: ERR2229190

Sample name:

Date: 31-03-2023 16:47:26

Number of reads: 562514

Percentage reads mapped: 99.13

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 6365 p.Gly376Cys missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
ccsA 620575 p.Ala229Ser missense_variant 0.33
ccsA 620690 p.Val267Gly missense_variant 0.29
rpoB 759893 c.87G>T synonymous_variant 0.2
rpoB 763056 p.Thr1084Ser missense_variant 0.22
rpoB 763069 p.Asp1088Val missense_variant 0.33
rpoC 764382 p.Ser338Tyr missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775808 c.2673C>A synonymous_variant 0.2
mmpL5 776080 p.Ala801Ser missense_variant 0.2
mmpL5 776081 c.2400G>A synonymous_variant 0.18
mmpL5 778852 c.-372C>A upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781570 p.Ile4Asn missense_variant 0.29
rpsL 781715 c.156T>C synonymous_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304628 c.1698G>T synonymous_variant 0.12
fbiC 1304905 p.Ala659Ser missense_variant 0.12
fbiC 1305020 p.Ala697Asp missense_variant 0.15
atpE 1461227 p.Glu61Asp missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474793 n.1136C>A non_coding_transcript_exon_variant 0.15
rrl 1476259 n.2602C>A non_coding_transcript_exon_variant 0.14
inhA 1674594 c.393C>T synonymous_variant 0.14
rpsA 1834011 p.Arg157Leu missense_variant 0.14
rpsA 1834853 p.Ala438Thr missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918265 p.Val109Gly missense_variant 0.17
tlyA 1918454 p.Ser172Leu missense_variant 0.12
ndh 2102646 p.Glu133* stop_gained 0.23
ndh 2103088 c.-46T>C upstream_gene_variant 0.12
PPE35 2167745 p.Thr956Arg missense_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.25
PPE35 2169272 c.1341C>G synonymous_variant 0.25
PPE35 2169278 c.1335T>C synonymous_variant 0.27
PPE35 2169281 c.1332T>G synonymous_variant 0.3
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2170035 p.Val193Ala missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.65
PPE35 2170053 p.Thr187Ser missense_variant 0.63
Rv1979c 2222564 p.Ser201Arg missense_variant 0.29
Rv1979c 2223102 p.Met21Ile missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519052 p.Thr313Met missense_variant 0.17
folC 2746986 p.Leu205Phe missense_variant 0.18
folC 2747250 p.Pro117Thr missense_variant 0.25
folC 2747562 p.Ser13Pro missense_variant 0.22
pepQ 2860210 p.Asp70Val missense_variant 0.15
whiB7 3568428 c.252A>G synonymous_variant 0.25
Rv3236c 3612958 c.159C>T synonymous_variant 0.33
Rv3236c 3613153 c.-37G>A upstream_gene_variant 0.29
fbiB 3642627 p.Arg365Ser missense_variant 0.12
alr 3840968 c.453G>A synonymous_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.21
rpoA 3877955 p.Gln185* stop_gained 0.17
clpC1 4039645 p.His354Asp missense_variant 0.2
clpC1 4039654 p.Thr351Ser missense_variant 0.2
clpC1 4040226 p.Gly160Val missense_variant 0.18
clpC1 4040472 p.Ile78Thr missense_variant 0.22
panD 4044232 p.Cys17Tyr missense_variant 0.17
embC 4239979 c.117A>T synonymous_variant 0.14
embC 4241276 c.1414C>T synonymous_variant 0.15
embC 4242074 p.Arg738Trp missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242690 p.Val943Asp missense_variant 0.2
embC 4242759 p.Pro966Gln missense_variant 0.15
embA 4244025 p.His265Asn missense_variant 0.15
embA 4245392 p.Lys720Asn missense_variant 0.29
embA 4245461 c.2229C>A synonymous_variant 0.2
embA 4245525 p.Gly765Arg missense_variant 0.15
embA 4246308 p.Thr1026Pro missense_variant 0.4
embB 4246836 p.Asp108Val missense_variant 0.14
embB 4247283 p.Arg257Leu missense_variant 0.18
embB 4247670 p.Ala386Glu missense_variant 0.13
embB 4248686 p.Gly725Arg missense_variant 0.15
ubiA 4269013 p.Pro274Arg missense_variant 0.17
ethA 4326227 p.Thr416Asn missense_variant 0.18
ethR 4326961 c.-588G>C upstream_gene_variant 0.17
ethR 4326964 c.-585G>A upstream_gene_variant 0.16
ethR 4326970 c.-579G>T upstream_gene_variant 0.17
whiB6 4338260 p.Arg88Trp missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407680 c.523C>A synonymous_variant 0.14
Rv3083 3448500 c.-3_*1408del transcript_ablation 1.0