TB-Profiler result

Run: ERR2229103
Summary

Run ID: ERR2229103

Sample name:

Date: 31-03-2023 16:38:53

Number of reads: 491568

Percentage reads mapped: 99.39

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7956 p.Val219Phe missense_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.4
mshA 576316 c.969A>T synonymous_variant 0.22
ccsA 620858 p.Val323Ala missense_variant 0.12
rpoB 760468 p.Asp221Gly missense_variant 0.12
rpoB 760990 p.Arg395Gln missense_variant 0.15
rpoB 762738 p.Glu978* stop_gained 0.13
rpoC 764348 p.Met327Leu missense_variant 0.4
rpoC 765733 c.2364G>T synonymous_variant 0.33
rpoC 766138 c.2769G>T synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775813 p.Phe890Val missense_variant 0.14
mmpL5 775817 c.2664T>C synonymous_variant 0.17
mmpL5 775820 c.2661G>A synonymous_variant 0.18
mmpL5 776594 c.1887G>T synonymous_variant 0.12
mmpL5 776835 p.Val549Asp missense_variant 0.12
mmpL5 778429 p.His18Tyr missense_variant 0.14
mmpR5 779033 p.Asp15Gly missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801091 p.Tyr95His missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305071 p.Asp714Val missense_variant 0.2
Rv1258c 1407076 p.Val89Ile missense_variant 0.29
atpE 1461246 p.Leu68Met missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473386 n.-272G>C upstream_gene_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474430 n.773C>A non_coding_transcript_exon_variant 0.5
rrl 1475612 n.1955G>T non_coding_transcript_exon_variant 0.29
rrl 1475901 n.2244C>A non_coding_transcript_exon_variant 0.29
fabG1 1673380 c.-60C>G upstream_gene_variant 0.28
rpsA 1833981 c.442delC frameshift_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154554 p.Thr520Ser missense_variant 0.13
katG 2154789 c.1323G>A synonymous_variant 0.25
katG 2155952 p.Val54Ile missense_variant 0.15
katG 2156436 c.-325C>T upstream_gene_variant 0.22
PPE35 2167745 p.Thr956Arg missense_variant 0.23
PPE35 2167814 c.2799C>T synonymous_variant 0.2
PPE35 2167865 c.2748G>C synonymous_variant 0.2
PPE35 2167868 c.2745A>C synonymous_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.14
PPE35 2169272 c.1341C>G synonymous_variant 0.14
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.14
PPE35 2169605 c.1008T>C synonymous_variant 0.11
PPE35 2169618 p.Phe332Cys missense_variant 0.11
PPE35 2169902 c.711G>C synonymous_variant 0.17
PPE35 2169910 p.Asn235Tyr missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.22
PPE35 2170053 p.Thr187Ser missense_variant 0.23
PPE35 2170147 p.Ser156Ala missense_variant 0.12
PPE35 2170157 p.Ala152Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288714 c.528C>T synonymous_variant 0.13
pncA 2289208 p.Asp12Tyr missense_variant 0.13
pncA 2290095 c.-854C>T upstream_gene_variant 0.18
eis 2714678 p.His219Asn missense_variant 0.15
Rv2752c 3064810 p.Thr461Asn missense_variant 0.15
thyX 3067811 p.Gln45His missense_variant 0.17
fbiD 3339364 p.Pro83Ala missense_variant 0.11
fbiD 3339374 p.Glu86Ala missense_variant 0.13
fbiD 3339393 c.276G>A synonymous_variant 0.14
Rv3083 3448333 c.-171G>A upstream_gene_variant 0.22
Rv3083 3448368 c.-136C>T upstream_gene_variant 0.18
Rv3236c 3612140 p.Ala326Val missense_variant 0.13
Rv3236c 3612446 p.Gly224Asp missense_variant 0.25
fbiA 3640954 p.Pro138Ala missense_variant 0.12
fbiB 3640965 c.-570C>G upstream_gene_variant 0.18
fbiB 3641541 p.Gly3Ser missense_variant 0.15
fbiB 3641783 c.249G>T synonymous_variant 0.22
rpoA 3877752 c.756C>T synonymous_variant 0.17
ddn 3987262 p.Thr140Asn missense_variant 0.13
clpC1 4039562 c.1143C>A synonymous_variant 0.12
panD 4044108 c.174C>T synonymous_variant 0.33
embC 4239821 c.-42C>A upstream_gene_variant 0.17
embC 4239826 c.-37T>A upstream_gene_variant 0.17
embC 4240332 p.Phe157Tyr missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245014 c.1782C>A synonymous_variant 0.17
embA 4245251 p.His673Gln missense_variant 0.11
embA 4246272 p.Thr1014Ala missense_variant 0.15
embB 4247790 p.Ser426Ile missense_variant 0.18
embB 4248513 p.Thr667Lys missense_variant 0.12
ethA 4326974 p.Trp167Leu missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0