TB-Profiler result

Run: ERR4816971
Summary

Run ID: ERR4816971

Sample name:

Date: 01-04-2023 14:44:25

Number of reads: 5989254

Percentage reads mapped: 94.94

Strain: lineage4.3.4.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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 0.73 streptomycin
katG 2155168 p.Ser315Thr missense_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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8715 p.Pro472Ser missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759608 c.-199C>T upstream_gene_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.11
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.14
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.21
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.14
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.23
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.12
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.12
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.14
rrs 1472437 n.592T>G non_coding_transcript_exon_variant 0.18
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.25
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.36
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.36
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.53
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.53
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.18
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.54
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.16
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.71
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.59
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.41
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.74
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.74
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.74
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.15
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.73
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.56
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.44
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.36
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.22
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.22
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.29
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.29
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.29
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.29
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.29
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.29
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.59
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.66
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.7
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.78
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.22
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.73
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.74
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.67
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.33
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.1
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.14
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.11
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.11
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.11
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.13
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.11
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.14
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.15
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.15
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.11
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.11
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.11
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.13
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.13
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.14
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.14
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.15
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.15
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.14
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.19
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.42
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.38
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.13
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2725969 c.-224_-223insG upstream_gene_variant 0.99
ahpC 2726323 p.Pro44Arg missense_variant 1.0
pepQ 2859830 p.Gly197Arg missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087518 c.699C>T synonymous_variant 0.99
Rv3083 3448598 p.Ile32Thr missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612768 p.Ala117Pro missense_variant 1.0
alr 3841006 p.Asp139His missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0