TB-Profiler result

Run: ERR4815040
Summary

Run ID: ERR4815040

Sample name:

Date: 01-04-2023 13:38:09

Number of reads: 944034

Percentage reads mapped: 90.13

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 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.93 streptomycin
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
mshA 575960 c.614delA frameshift_variant 0.11
mshA 576077 c.730C>T synonymous_variant 1.0
ccsA 620532 c.642T>G synonymous_variant 0.18
rpoC 764315 p.Ala316Ser missense_variant 0.11
rpoC 766543 c.3174C>T synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778209 p.Ala91Val missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472105 n.260T>C non_coding_transcript_exon_variant 0.18
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.13
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.23
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.29
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.29
rrs 1472274 n.429A>G non_coding_transcript_exon_variant 0.29
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.33
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.5
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 1.0
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.92
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.93
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.93
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.95
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.95
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.98
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.98
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.95
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.97
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 1.0
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.97
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 1.0
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.97
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.98
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.94
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.94
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.91
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.91
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.96
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 1.0
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 1.0
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 1.0
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.33
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.33
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.5
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.33
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.5
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.33
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.33
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.33
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.33
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.6
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.6
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.6
rrs 1473109 n.1264T>C non_coding_transcript_exon_variant 0.4
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.6
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.6
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.5
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.5
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.27
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.21
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.19
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.26
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.22
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.33
rrs 1473201 n.1356A>G non_coding_transcript_exon_variant 0.14
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.18
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.24
rrs 1473258 n.1413T>C non_coding_transcript_exon_variant 0.13
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.13
rrs 1473263 n.1418A>G non_coding_transcript_exon_variant 0.13
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.15
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153931 c.2181C>A synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290201 c.-960G>A upstream_gene_variant 0.13
kasA 2518556 p.Asn148Tyr missense_variant 0.12
ahpC 2726350 p.Trp53Leu missense_variant 0.18
folC 2746573 p.Met342Ile missense_variant 0.11
pepQ 2859580 p.Leu280Pro missense_variant 0.11
pepQ 2859640 p.Gly260Asp missense_variant 0.12
ribD 2987390 c.552T>C synonymous_variant 0.12
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474720 c.714G>A synonymous_variant 0.11
Rv3236c 3612004 c.1113C>T synonymous_variant 0.11
embC 4242236 p.Ala792Thr missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244134 p.Glu301Gly missense_variant 0.1
aftB 4267883 c.954C>T synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338599 c.-78A>C upstream_gene_variant 1.0