TB-Profiler result

Run: ERR1462610
Summary

Run ID: ERR1462610

Sample name:

Date: 31-03-2023 14:13:05

Number of reads: 6336638

Percentage reads mapped: 60.67

Strain: La2

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
La2 M.caprae None None 0.99
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 0.56 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
gyrB 5752 c.513G>A synonymous_variant 1.0
gyrA 6307 c.-995T>G upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 0.98
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759719 c.-88C>A upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.12
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.12
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.13
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.15
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.15
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.14
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.14
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.16
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.19
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.18
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.34
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.33
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.35
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.34
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.48
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.53
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.52
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.52
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.47
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.47
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.42
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.13
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.3
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.33
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.56
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.56
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.55
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.53
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.49
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.11
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.16
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.16
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.16
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.16
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.15
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.15
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.12
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.1
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.11
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.11
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.11
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.11
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.13
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.13
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.14
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.15
rrl 1476048 n.2392dupC non_coding_transcript_exon_variant 1.0
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.35
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.35
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.46
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.49
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.57
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.61
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.61
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.68
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.68
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.67
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.54
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.44
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.37
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.32
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.32
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.3
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.3
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.27
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.27
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.27
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.27
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.27
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.19
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.1
inhA 1673766 c.-436C>T upstream_gene_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.98
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
katG 2156308 c.-197G>A upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168364 p.Thr750Met missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.98
eis 2714317 p.Arg339Gln missense_variant 0.99
folC 2747197 c.402C>T synonymous_variant 1.0
pepQ 2860555 c.-137A>G upstream_gene_variant 0.99
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
ald 3087084 c.266delA frameshift_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.99
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 0.99
ubiA 4269088 p.Ala249Val missense_variant 1.0
aftB 4269150 c.-314G>T upstream_gene_variant 0.99
aftB 4269351 c.-515C>T upstream_gene_variant 0.99
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99