TB-Profiler result

Run: SRR14164490
Summary

Run ID: SRR14164490

Sample name:

Date: 03-04-2023 09:53:48

Number of reads: 1059660

Percentage reads mapped: 98.84

Strain: lineage4.4.1.1

Drug-resistance: HR-TB

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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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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
katG 2154376 c.1735delA frameshift_variant 0.14 isoniazid
ahpC 2726119 c.-74G>A upstream_gene_variant 1.0 isoniazid
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 5846 p.Gly203Trp missense_variant 0.15
gyrB 7159 p.Asp640Glu missense_variant 0.18
gyrA 7178 c.-124T>C upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.5
mshA 576365 p.Phe340Leu missense_variant 0.11
ccsA 620044 p.Gly52Arg missense_variant 0.14
rpoB 762487 p.Pro894Leu missense_variant 0.11
rpoC 764533 c.1164C>T synonymous_variant 0.18
rpoC 765812 c.2443C>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777262 p.Thr407Ser missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801427 p.Met207Leu missense_variant 0.11
fbiC 1304517 c.1587C>T synonymous_variant 0.11
atpE 1461001 c.-44G>T upstream_gene_variant 0.15
atpE 1461260 c.216G>A synonymous_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.33
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.33
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.33
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.38
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.38
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.43
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.43
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.19
rrl 1476609 n.2952G>A non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918435 p.Ala166Pro missense_variant 0.11
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168417 c.2196C>T synonymous_variant 0.17
PPE35 2168488 p.Ile709Val missense_variant 0.18
PPE35 2168859 p.Ser585Ile missense_variant 0.12
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170130 c.481_482dupGT frameshift_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289903 c.-662C>T upstream_gene_variant 0.2
kasA 2518808 p.Lys232Glu missense_variant 0.22
eis 2715394 c.-62C>T upstream_gene_variant 0.14
ahpC 2725926 c.-267T>C upstream_gene_variant 0.12
folC 2746198 c.1401C>T synonymous_variant 0.13
ribD 2987161 p.Ala108Val missense_variant 0.12
ribD 2987448 p.Glu204Lys missense_variant 0.15
thyA 3073880 p.Glu198Lys missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339200 p.Pro28Leu missense_variant 0.12
fbiD 3339734 p.Ala206Gly missense_variant 0.25
Rv3083 3448423 c.-81C>G upstream_gene_variant 0.11
Rv3083 3448523 p.Val7Asp missense_variant 0.2
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3448718 p.Val72Gly missense_variant 0.12
Rv3083 3448743 c.240G>C synonymous_variant 0.12
Rv3083 3449059 p.Gly186Ser missense_variant 0.13
Rv3083 3449762 p.Val420Ala missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474590 p.Val195Ala missense_variant 0.11
whiB7 3568682 c.-3G>A upstream_gene_variant 0.13
whiB7 3568844 c.-165C>G upstream_gene_variant 0.12
Rv3236c 3612357 p.Glu254Lys missense_variant 0.18
Rv3236c 3612556 c.561G>A synonymous_variant 0.14
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiA 3640819 p.Val93* stop_gained 0.11
fbiB 3641782 p.Val83Ala missense_variant 0.18
rpoA 3877919 p.Glu197Lys missense_variant 1.0
embC 4240413 p.Leu184Arg missense_variant 0.22
embC 4241451 p.Ser530Leu missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243673 c.441C>T synonymous_variant 0.29
embA 4245461 c.2229C>T synonymous_variant 1.0
embB 4246903 c.390G>T synonymous_variant 0.11
embB 4249573 c.3060T>G synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407838 p.Ser122Phe missense_variant 0.11