TB-Profiler result

Run: ERR4820711
Summary

Run ID: ERR4820711

Sample name:

Date: 01-04-2023 16:50:05

Number of reads: 405356

Percentage reads mapped: 95.45

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H 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 0.75 streptomycin
katG 2154022 c.2089delG frameshift_variant 0.29 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 5105 c.-135G>A upstream_gene_variant 0.11
gyrB 5637 p.Thr133Ser missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575767 c.420G>A synonymous_variant 0.2
ccsA 620748 c.858T>G synonymous_variant 0.29
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 763991 p.Ile208Val missense_variant 0.29
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765953 p.Asp862Asn missense_variant 0.2
rpoC 766058 p.Ile897Val missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303784 p.Gly285Glu missense_variant 0.11
embR 1416202 c.1146G>T synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471799 n.-47A>T upstream_gene_variant 0.12
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 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 1472655 n.810G>A non_coding_transcript_exon_variant 0.8
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.67
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.67
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.67
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.67
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.4
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.67
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.5
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.75
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.4
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.75
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.29
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.75
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.75
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.67
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.67
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 1.0
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>C 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 1.0
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 1.0
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 1476337 n.2680C>T non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 1.0
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 1.0
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 1.0
inhA 1674739 p.Gly180Ser missense_variant 0.18
rpsA 1834837 p.Met432Ile missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101897 c.1146C>T synonymous_variant 0.17
ndh 2102285 p.Asp253Gly missense_variant 0.17
katG 2154840 c.1272G>A synonymous_variant 0.2
katG 2156483 c.-372C>T upstream_gene_variant 0.12
PPE35 2168405 c.2208G>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518723 c.609G>A synonymous_variant 0.5
ahpC 2725942 c.-251C>G upstream_gene_variant 0.22
ahpC 2725986 c.-207C>T upstream_gene_variant 0.15
ahpC 2726135 c.-58A>G upstream_gene_variant 0.12
ahpC 2726265 p.Lys25Gln missense_variant 0.33
ahpC 2726623 p.Ile144Thr missense_variant 0.25
folC 2747099 p.Pro167Leu missense_variant 0.14
pepQ 2859997 p.Ala141Val missense_variant 0.22
pepQ 2860171 p.Leu83Pro missense_variant 0.5
ribD 2987148 p.Gln104Lys missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087143 c.324G>A synonymous_variant 0.29
ald 3087874 p.Ser352Phe missense_variant 0.25
Rv3083 3448631 p.Gly43Ala missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568866 c.-187C>A upstream_gene_variant 0.17
Rv3236c 3612351 p.Ala256Thr missense_variant 0.5
Rv3236c 3612679 c.438G>A synonymous_variant 0.25
Rv3236c 3613030 c.87G>A synonymous_variant 0.33
fbiB 3640545 c.-990G>A upstream_gene_variant 0.33
fbiB 3641562 p.Ser10Thr missense_variant 0.12
fbiB 3641989 p.Met152Arg missense_variant 0.2
alr 3840687 p.Asp245Gly missense_variant 0.18
clpC1 4040753 c.-49G>A upstream_gene_variant 0.17
embC 4240648 c.786C>T synonymous_variant 0.38
embC 4241802 p.Gly647Asp missense_variant 0.14
embC 4242398 p.Ala846Thr missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246834 p.Lys107Asn missense_variant 0.18
embB 4247904 p.Arg464Pro missense_variant 0.17
embB 4249385 p.Glu958Lys missense_variant 0.15
aftB 4267151 c.1686C>A synonymous_variant 0.18
ethR 4327450 c.-99G>C upstream_gene_variant 0.29
ethA 4328212 c.-739G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0