TB-Profiler result

Run: ERR3077935
Summary

Run ID: ERR3077935

Sample name:

Date: 01-04-2023 00:11:35

Number of reads: 620664

Percentage reads mapped: 98.65

Strain: lineage4.2.2.2

Drug-resistance: Other

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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
lineage4.2 Euro-American H;T;LAM None 0.99
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
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
pncA 2288823 p.Arg140His missense_variant 0.12 pyrazinamide
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9307 p.Asp669Gly missense_variant 0.11
mshA 575589 p.Arg81His missense_variant 0.13
mshA 576077 c.730C>T synonymous_variant 1.0
ccsA 619694 c.-197C>T upstream_gene_variant 0.5
ccsA 620228 p.Phe113Ser missense_variant 0.14
rpoB 761489 c.1683G>A synonymous_variant 1.0
rpoB 763147 p.Ser1114Leu missense_variant 0.13
rpoC 765468 c.2101delG frameshift_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776573 c.1908G>T synonymous_variant 0.11
mmpL5 777087 p.Ile465Asn missense_variant 0.11
mmpL5 777404 c.1077C>G synonymous_variant 0.25
mmpL5 777888 p.Gln198Arg missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781896 p.Ala113Pro missense_variant 0.1
fbiC 1303652 p.Arg241Gln missense_variant 0.11
atpE 1461075 p.Ile11Val missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 1.0
rrl 1475447 n.1790A>G non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918136 p.Gly66Val missense_variant 0.22
tlyA 1918509 c.570T>C synonymous_variant 0.11
ndh 2102727 p.His106Tyr missense_variant 0.11
ndh 2103187 c.-145G>A upstream_gene_variant 0.13
PPE35 2167945 p.Ser890Pro missense_variant 0.11
Rv1979c 2222517 c.648C>T synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518465 c.351T>A synonymous_variant 0.18
kasA 2518540 c.426T>C synonymous_variant 0.13
kasA 2518574 p.Ile154Val missense_variant 0.18
eis 2715223 p.Arg37Gln missense_variant 0.13
eis 2715367 c.-35G>A upstream_gene_variant 0.11
pepQ 2860075 p.Glu115Gly missense_variant 0.11
ribD 2986887 p.Leu17Val missense_variant 0.17
Rv2752c 3065553 c.639A>T synonymous_variant 0.12
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.93
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087888 p.Thr357Ala missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475101 c.1095C>G synonymous_variant 0.13
Rv3236c 3612736 c.381T>C synonymous_variant 0.11
fbiA 3640979 p.Thr146Ile missense_variant 0.12
alr 3840503 c.918T>C synonymous_variant 0.11
ddn 3986723 c.-121G>A upstream_gene_variant 0.12
ddn 3987046 p.Arg68His missense_variant 0.11
clpC1 4039590 p.Val372Ala missense_variant 0.11
clpC1 4040688 p.Thr6Ser missense_variant 0.11
panD 4044429 c.-148C>G upstream_gene_variant 0.15
embC 4240646 p.Phe262Val missense_variant 0.2
embC 4242458 p.Ser866Pro missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246386 p.Arg1052Gly missense_variant 0.11
embB 4247439 p.Val309Asp missense_variant 0.1
aftB 4268536 p.Gly101Arg missense_variant 0.14
ubiA 4269977 c.-144C>A upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0