TB-Profiler result

Run: ERR4820918
Summary

Run ID: ERR4820918

Sample name:

Date: 01-04-2023 16:57:25

Number of reads: 214403

Percentage reads mapped: 60.81

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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 0.97 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 7909 p.Trp203* stop_gained 0.29
mshA 576456 p.Val370Ala missense_variant 0.5
rpoC 766746 c.3382delC frameshift_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776117 p.Phe788Leu missense_variant 0.4
mmpS5 778965 c.-60G>A upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800679 c.-130T>G upstream_gene_variant 0.33
embR 1416864 p.Phe162Leu missense_variant 0.33
atpE 1460912 c.-133C>T upstream_gene_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 1.0
rrs 1472123 n.278A>G non_coding_transcript_exon_variant 1.0
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 1.0
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 1.0
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 1.0
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.5
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
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 0.97
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 1472616 n.771G>A non_coding_transcript_exon_variant 0.3
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.5
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.97
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 1.0
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
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 0.87
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.71
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.71
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 1.0
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 1.0
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 1.0
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 1.0
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 1.0
rrl 1474275 n.618T>C non_coding_transcript_exon_variant 1.0
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.5
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 1.0
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.65
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.65
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101877 p.Gly389Asp missense_variant 0.67
katG 2155233 c.879G>T synonymous_variant 0.5
katG 2155907 p.Ala69Ser missense_variant 0.5
katG 2155941 c.171G>A synonymous_variant 0.33
PPE35 2169179 c.1434C>T synonymous_variant 0.29
Rv1979c 2222671 c.493delA frameshift_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518403 p.Ser97Thr missense_variant 0.5
pepQ 2860373 p.Ala16Ser missense_variant 0.29
pepQ 2860459 c.-41T>C upstream_gene_variant 0.25
ribD 2986882 p.Arg15Lys missense_variant 1.0
thyX 3067279 p.Ala223Thr missense_variant 0.22
thyA 3073895 p.Gly193Ser missense_variant 1.0
Rv3083 3449457 c.954C>T synonymous_variant 0.4
fbiA 3640723 p.Asp61Asn missense_variant 0.33
alr 3840696 p.Ala242Val missense_variant 0.67
ddn 3987104 p.Met87Ile missense_variant 1.0
clpC1 4040234 c.471C>T synonymous_variant 0.67
panD 4044284 c.-3C>A upstream_gene_variant 1.0
panD 4044435 c.-154C>T upstream_gene_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245034 p.Arg601Leu missense_variant 0.2
aftB 4269393 c.-557G>T upstream_gene_variant 0.29
ethA 4328358 c.-885C>T upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408000 c.202delA frameshift_variant 0.29