TB-Profiler result

Run: ERR2228821
Summary

Run ID: ERR2228821

Sample name:

Date: 31-03-2023 16:22:03

Number of reads: 784995

Percentage reads mapped: 99.36

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
mshA 576330 p.Leu328Gln missense_variant 0.23
rpoC 766892 p.Phe1175Leu missense_variant 0.22
rpoC 766910 p.Ile1181Leu missense_variant 0.33
rpoC 766914 p.Asp1182Ala missense_variant 0.22
rpoC 766938 p.Asn1190Ile missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776027 c.2454G>A synonymous_variant 0.14
mmpL5 776030 c.2451G>A synonymous_variant 0.14
mmpL5 776751 p.Phe577Ser missense_variant 0.17
mmpL5 778919 c.-439A>T upstream_gene_variant 0.44
mmpR5 779125 p.Cys46Arg missense_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801077 p.Asp90Gly missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304216 p.Asn429Thr missense_variant 0.25
fbiC 1304981 p.Lys684Met missense_variant 0.33
atpE 1461143 p.Asn33Lys missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.22
rrl 1473885 n.228A>T non_coding_transcript_exon_variant 0.33
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475388 n.1731A>T non_coding_transcript_exon_variant 0.38
rrl 1475567 n.1914delA non_coding_transcript_exon_variant 0.17
fabG1 1673329 c.-111A>C upstream_gene_variant 0.27
fabG1 1673642 p.Val68Gly missense_variant 0.22
fabG1 1674006 p.Asp189Glu missense_variant 0.33
inhA 1674356 p.Asp52Ala missense_variant 0.33
inhA 1674371 p.Lys57Thr missense_variant 0.4
inhA 1674400 p.Asn67Tyr missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918453 p.Ser172Ala missense_variant 0.12
ndh 2102411 p.Val211Gly missense_variant 0.14
ndh 2102471 p.Glu191Ala missense_variant 0.16
katG 2155660 p.Val151Gly missense_variant 0.19
PPE35 2168586 p.Ile676Asn missense_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169017 p.Leu532Phe missense_variant 0.21
PPE35 2169031 p.Asp528Tyr missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.13
PPE35 2170436 c.177T>G synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289826 c.-585A>T upstream_gene_variant 0.2
kasA 2518605 p.Val164Gly missense_variant 0.17
folC 2746281 p.Ile440Phe missense_variant 0.18
folC 2746331 p.Glu423Ala missense_variant 0.22
folC 2747056 p.Trp181Cys missense_variant 0.25
pepQ 2859490 p.Val310Gly missense_variant 0.31
pepQ 2860101 c.318C>A synonymous_variant 0.14
Rv2752c 3064717 p.Leu492Gln missense_variant 0.67
Rv2752c 3065638 p.Leu185Gln missense_variant 0.25
ald 3087763 p.Asn315Thr missense_variant 0.28
fbiD 3339253 p.Thr46Ser missense_variant 0.27
fbiD 3339422 p.Val102Glu missense_variant 0.4
fprA 3474769 p.Tyr255Asp missense_variant 0.12
Rv3236c 3612569 p.Val183Gly missense_variant 0.6
Rv3236c 3612862 p.Ser85Arg missense_variant 0.21
fbiB 3641857 p.Val108Gly missense_variant 0.27
fbiB 3642837 p.Leu435Val missense_variant 0.14
alr 3840384 p.Phe346Ser missense_variant 0.13
alr 3840588 p.Lys278Ile missense_variant 0.17
rpoA 3878040 c.468T>A synonymous_variant 0.25
rpoA 3878490 c.18C>G synonymous_variant 0.4
clpC1 4040031 p.Val225Gly missense_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242645 p.Asn928Thr missense_variant 0.31
embA 4244817 p.Phe529Ile missense_variant 0.5
embA 4245568 p.Glu779Ala missense_variant 0.29
embA 4245655 p.Asp808Ala missense_variant 0.4
embB 4246544 p.Thr11Pro missense_variant 0.12
aftB 4267756 p.Lys361* stop_gained 0.25
ubiA 4268986 p.Val283Gly missense_variant 0.14
ubiA 4269043 p.Val264Gly missense_variant 0.27
ethA 4327365 p.Lys37* stop_gained 0.17
ethR 4328104 p.Ser186Ala missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0