TB-Profiler result

Run: ERR4819481
Summary

Run ID: ERR4819481

Sample name:

Date: 01-04-2023 16:08:02

Number of reads: 613910

Percentage reads mapped: 91.73

Strain: lineage4.3.3

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 1.0 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 5169 c.-71G>A upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759827 c.25delA frameshift_variant 0.15
rpoB 761492 c.1686G>A synonymous_variant 0.13
rpoB 761495 p.Glu563Asp missense_variant 1.0
rpoC 763684 p.Trp105Cys missense_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775687 p.Leu932Ile missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305391 p.Gly821Ser missense_variant 0.18
Rv1258c 1406911 p.Gly144Ser missense_variant 0.12
embR 1416891 c.457C>T synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 1.0
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.67
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.67
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.67
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.67
rrs 1472251 n.406G>A 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 0.86
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.88
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.88
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.83
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.92
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.83
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.86
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.42
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.92
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.92
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.8
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
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 1472895 n.1050C>T non_coding_transcript_exon_variant 1.0
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.6
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.4
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.6
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 1.0
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 1.0
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 1.0
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.57
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.57
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 1.0
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.25
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.33
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.88
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.86
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.88
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 1.0
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.75
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.86
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.8
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.8
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.8
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.67
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.67
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.67
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.56
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.62
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.45
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.67
rrl 1474249 n.592G>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 0.75
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.8
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.8
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.4
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.4
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.5
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.5
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.5
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.5
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.5
rpsA 1834445 p.Thr302Ser missense_variant 0.12
rpsA 1834660 c.1119C>T synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168611 p.Asn668Asp missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyX 3068153 c.-208G>T upstream_gene_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086899 p.Thr27Ser missense_variant 0.15
fbiD 3339363 p.Asp82Glu missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568554 c.126G>T synonymous_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244337 p.Leu369Met missense_variant 0.15
embB 4245791 c.-723C>A upstream_gene_variant 0.2
embB 4246916 p.Val135Met missense_variant 0.12
embB 4247653 c.1143delA frameshift_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0