TB-Profiler result

Run: ERR1949956

Summary

Run ID: ERR1949956

Sample name:

Date: 31-03-2023 15:35:40

Number of reads: 730407

Percentage reads mapped: 98.39

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
gyrB 5986 c.747C>G synonymous_variant 0.14
gyrB 6169 c.930C>A synonymous_variant 0.29
gyrB 6388 p.Phe383Leu missense_variant 0.29
gyrA 6730 c.-572A>T upstream_gene_variant 0.29
gyrB 7152 p.Leu638Arg missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9114 p.Glu605Gln missense_variant 0.12
fgd1 491297 p.Val172Gly missense_variant 0.5
fgd1 491315 p.Gly178Ala missense_variant 0.33
mshA 575475 p.Asp43Ala missense_variant 0.17
mshA 575824 c.477T>G synonymous_variant 0.25
mshA 576264 p.Leu306Gln missense_variant 0.18
mshA 576489 p.Val381Glu missense_variant 0.3
rpoB 761143 p.Lys446Met missense_variant 0.31
rpoB 762694 p.Asn963Ile missense_variant 0.33
rpoC 766481 c.3112C>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775801 p.Ser894Ala missense_variant 0.29
mmpL5 777119 p.His454Gln missense_variant 0.15
mmpL5 777187 p.Ala432Ser missense_variant 0.22
mmpL5 777713 c.768T>A synonymous_variant 0.23
mmpL5 777879 p.Asp201Ala missense_variant 0.2
mmpL5 778615 c.-135G>A upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781698 p.Ser47Pro missense_variant 0.12
rpsL 781717 p.Ala53Asp missense_variant 0.15
fbiC 1303676 p.Gly249Ala missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 0.95
fbiC 1304974 p.Lys682* stop_gained 0.33
Rv1258c 1407033 p.Val103Gly missense_variant 0.21
Rv1258c 1407039 p.Val101Gly missense_variant 0.42
atpE 1461045 c.1A>T initiator_codon_variant 0.33
atpE 1461230 c.186G>C synonymous_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471904 n.59T>A non_coding_transcript_exon_variant 0.29
rrs 1472090 n.245A>T non_coding_transcript_exon_variant 0.2
rrl 1473594 n.-64A>T upstream_gene_variant 0.22
rrl 1473940 n.283A>T non_coding_transcript_exon_variant 0.29
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.12
rrl 1475355 n.1698C>G non_coding_transcript_exon_variant 0.22
rrl 1475755 n.2098T>A non_coding_transcript_exon_variant 0.5
rrl 1476731 n.3074G>C non_coding_transcript_exon_variant 0.33
inhA 1674284 p.Val28Ala missense_variant 0.15
rpsA 1834309 c.768C>T synonymous_variant 0.15
rpsA 1834753 c.1212T>C synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918499 p.Val187Gly missense_variant 0.15
tlyA 1918529 p.Val197Gly missense_variant 0.17
ndh 2102604 c.439T>C synonymous_variant 0.17
ndh 2102610 c.433T>C synonymous_variant 0.17
ndh 2102635 c.408C>G synonymous_variant 0.2
ndh 2102638 c.405A>G synonymous_variant 0.27
ndh 2102644 c.399A>G synonymous_variant 0.17
ndh 2102697 p.Ile116Leu missense_variant 0.25
katG 2154040 p.Gly691Asp missense_variant 0.17
katG 2154710 p.Thr468Pro missense_variant 0.29
katG 2155859 p.Thr85Ala missense_variant 0.2
PPE35 2167783 p.Ser944Pro missense_variant 0.29
PPE35 2168144 c.2469G>A synonymous_variant 0.4
PPE35 2168681 p.Phe644Leu missense_variant 0.36
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169031 p.Asp528Tyr missense_variant 0.33
PPE35 2169125 p.Val496Ile missense_variant 0.18
PPE35 2169773 c.840C>A synonymous_variant 0.25
PPE35 2170092 p.Leu174Arg missense_variant 0.15
Rv1979c 2222011 p.Gln385Leu missense_variant 0.25
Rv1979c 2222103 c.1062A>G synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289792 c.-551A>T upstream_gene_variant 0.22
kasA 2518300 c.186T>C synonymous_variant 0.25
kasA 2518588 c.474T>C synonymous_variant 0.15
kasA 2518783 c.669T>A synonymous_variant 0.21
kasA 2519260 c.1146T>A synonymous_variant 0.25
folC 2746760 p.Gln280Leu missense_variant 0.22
folC 2747290 c.309A>C synonymous_variant 0.18
pepQ 2860098 c.321G>C synonymous_variant 0.22
pepQ 2860542 c.-124T>C upstream_gene_variant 0.33
ribD 2987453 c.615T>G synonymous_variant 0.23
Rv2752c 3065464 p.Asp243Val missense_variant 0.2
thyX 3067304 p.Glu214Asp missense_variant 0.38
thyX 3067470 p.Asn159Thr missense_variant 0.33
thyX 3067475 p.Gln157His missense_variant 0.29
thyX 3067599 p.Val116Gly missense_variant 0.14
thyA 3073683 c.789A>G synonymous_variant 0.13
fprA 3474247 p.Asn81Tyr missense_variant 0.6
fprA 3475283 p.Ile426Ser missense_variant 0.22
Rv3236c 3612243 p.Pro292Thr missense_variant 0.17
Rv3236c 3612478 c.639T>A synonymous_variant 0.29
fbiA 3640495 c.-48T>C upstream_gene_variant 0.22
alr 3841545 c.-125G>A upstream_gene_variant 0.15
rpoA 3878355 c.153C>G synonymous_variant 0.2
rpoA 3878453 p.Ser19Thr missense_variant 0.22
clpC1 4039730 c.975C>G synonymous_variant 0.12
clpC1 4040524 p.Ser61Cys missense_variant 0.3
clpC1 4040527 p.Arg60Ser missense_variant 0.18
embC 4242429 p.Ala856Asp missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243912 p.Leu227Arg missense_variant 0.33
embB 4247076 p.Val188Gly missense_variant 0.22
embB 4247470 c.957T>C synonymous_variant 0.15
embB 4248918 p.Ile802Ser missense_variant 0.13
aftB 4267774 p.Ile355Phe missense_variant 0.33
aftB 4267945 p.Tyr298Asp missense_variant 0.17
aftB 4268619 p.Val73Gly missense_variant 0.2
ubiA 4269271 p.Val188Ala missense_variant 0.12
ethA 4326911 p.Val188Ala missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0