TB-Profiler result

Run: ERR1950011
Summary

Run ID: ERR1950011

Sample name:

Date: 31-03-2023 15:37:24

Number of reads: 574080

Percentage reads mapped: 99.66

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 6747 p.Gln503Leu missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 490892 p.Val37Gly missense_variant 0.18
rpoC 766274 p.Ala969Thr missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776401 p.Glu694Lys missense_variant 0.18
mmpL5 777245 c.1236G>T synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801031 p.Val75Phe missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473407 n.-251A>G upstream_gene_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474621 n.964A>G non_coding_transcript_exon_variant 0.13
rrl 1474802 n.1145T>A non_coding_transcript_exon_variant 0.11
rrl 1474925 n.1268G>A non_coding_transcript_exon_variant 0.12
fabG1 1673708 p.Gly90Asp missense_variant 0.17
rpsA 1834555 c.1014T>C synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102130 p.Val305Met missense_variant 0.18
ndh 2102175 c.867delT frameshift_variant 0.13
katG 2154877 p.Trp412Leu missense_variant 0.25
katG 2155193 p.Gly307* stop_gained 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168876 p.Phe579Leu missense_variant 0.17
PPE35 2168971 p.Ile548Val missense_variant 0.14
PPE35 2170447 p.Ser56Ala missense_variant 0.67
Rv1979c 2222530 p.Glu212Val missense_variant 0.11
Rv1979c 2222842 c.322delG frameshift_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288746 p.Asp166His missense_variant 0.1
folC 2747747 c.-149C>A upstream_gene_variant 0.11
pepQ 2860307 p.Gly38Trp missense_variant 0.33
pepQ 2860316 p.Gly35Cys missense_variant 0.33
pepQ 2860583 c.-165G>A upstream_gene_variant 0.15
ribD 2986869 p.Asp11Asn missense_variant 0.12
Rv2752c 3064566 c.1626G>C synonymous_variant 0.43
Rv2752c 3065476 p.Ala239Asp missense_variant 0.12
Rv2752c 3066996 c.-805T>C upstream_gene_variant 0.12
fprA 3475231 p.Trp409Arg missense_variant 0.12
Rv3236c 3612289 c.828G>C synonymous_variant 0.18
Rv3236c 3612374 p.Gly248Val missense_variant 0.14
Rv3236c 3612890 p.Glu76Gly missense_variant 0.11
Rv3236c 3612997 c.120T>G synonymous_variant 0.14
fbiA 3640880 p.Leu113Arg missense_variant 0.13
fbiA 3640888 c.349delC frameshift_variant 0.25
fbiA 3640915 p.Leu125Met missense_variant 0.13
fbiA 3641059 p.Trp173Arg missense_variant 0.12
fbiB 3641598 p.Glu22Lys missense_variant 0.12
fbiB 3641848 p.Ala105Val missense_variant 0.2
alr 3840676 p.Asp249Asn missense_variant 0.17
alr 3841327 p.Pro32Ser missense_variant 0.1
clpC1 4039409 c.1296T>A synonymous_variant 0.4
embC 4240035 p.Gln58Arg missense_variant 0.12
embC 4241223 p.Gly454Val missense_variant 0.11
embC 4241790 p.Val643Ala missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242903 p.Asp1014Gly missense_variant 0.11
embA 4244752 c.1522delG frameshift_variant 0.12
embA 4245715 p.Leu828Gln missense_variant 0.18
ubiA 4269188 p.Thr216Ser missense_variant 0.13
aftB 4269327 c.-491A>G upstream_gene_variant 0.12
ubiA 4269383 p.Cys151Arg missense_variant 0.13
whiB6 4338261 c.261G>C synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408031 p.Leu58Ile missense_variant 0.11
gid 4408060 p.His48Arg missense_variant 0.11
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0