TB-Profiler result

Run: ERR2229801
Summary

Run ID: ERR2229801

Sample name:

Date: 31-03-2023 17:35:57

Number of reads: 158083

Percentage reads mapped: 65.56

Strain: lineage4

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
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 1473247 n.1402C>A non_coding_transcript_exon_variant 0.6 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.33 kanamycin, capreomycin, aminoglycosides, amikacin
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 7326 p.Asp9Asn missense_variant 0.5
gyrA 9695 c.2394C>A synonymous_variant 0.4
mshA 575888 p.Ala181Ser missense_variant 0.25
rpoB 760497 p.Leu231Met missense_variant 0.25
rpoC 763528 c.159G>A synonymous_variant 1.0
rpoC 763534 c.165T>C synonymous_variant 1.0
rpoC 763537 c.168C>G synonymous_variant 1.0
rpoC 763546 c.177A>G synonymous_variant 1.0
rpoC 763570 c.201G>C synonymous_variant 0.67
rpoC 763573 c.204G>C synonymous_variant 0.67
rpoC 763594 c.225C>T synonymous_variant 0.75
rpoC 763622 p.Ala85Ser missense_variant 0.67
rpoC 763627 p.Lys86Asn missense_variant 0.67
rpoC 763642 c.273G>T synonymous_variant 0.57
rpoC 763648 c.279C>A synonymous_variant 0.57
rpoC 766237 c.2868T>A synonymous_variant 0.33
rpoC 766270 c.2901G>A synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800899 p.Ala31Ser missense_variant 0.15
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304361 c.1431C>G synonymous_variant 0.22
fbiC 1304768 p.Gly613Asp missense_variant 0.2
fbiC 1304812 p.Met628Val missense_variant 0.18
fbiC 1304984 p.Leu685Pro missense_variant 0.29
fbiC 1305457 p.Pro843Thr missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.5
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.67
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.33
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.33
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.33
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.33
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.33
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.33
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.33
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.43
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.43
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 1.0
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 1.0
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.86
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.86
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 1.0
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.75
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.75
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.75
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.56
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.6
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.4
rrs 1473091 n.1246G>A non_coding_transcript_exon_variant 0.4
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.4
rrs 1473094 n.1249T>G non_coding_transcript_exon_variant 0.4
rrs 1473099 n.1254T>G non_coding_transcript_exon_variant 0.4
rrs 1473100 n.1255G>C non_coding_transcript_exon_variant 0.4
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.4
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.4
rrs 1473109 n.1264T>G non_coding_transcript_exon_variant 0.4
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.4
rrs 1473120 n.1275C>T non_coding_transcript_exon_variant 0.4
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.4
rrs 1473122 n.1277T>G non_coding_transcript_exon_variant 0.4
rrs 1473123 n.1278A>G non_coding_transcript_exon_variant 0.4
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.67
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.67
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.67
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.5
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.6
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.43
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.43
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.43
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.43
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.43
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.43
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.33
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.33
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.33
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.33
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474454 n.797G>A non_coding_transcript_exon_variant 0.5
rrl 1474467 n.810A>T non_coding_transcript_exon_variant 0.57
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.57
rrl 1474488 n.831G>A non_coding_transcript_exon_variant 0.57
rrl 1474496 n.839C>T non_coding_transcript_exon_variant 0.67
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.67
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.57
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.57
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.57
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.57
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.57
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.57
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.57
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.57
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.57
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.57
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.67
rrl 1474669 n.1012G>T non_coding_transcript_exon_variant 1.0
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.71
rrl 1474752 n.1096delA non_coding_transcript_exon_variant 0.71
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.71
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.71
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.71
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.71
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.6
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.6
rrl 1474799 n.1143delT non_coding_transcript_exon_variant 0.6
rrl 1474803 n.1146_1147insA non_coding_transcript_exon_variant 0.6
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.6
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.75
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.75
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.75
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.75
rrl 1475317 n.1660G>T non_coding_transcript_exon_variant 0.67
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.75
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.75
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.75
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.8
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.67
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.67
inhA 1674786 c.585G>T synonymous_variant 0.18
rpsA 1833928 c.387G>C synonymous_variant 0.22
rpsA 1833952 c.411C>A synonymous_variant 0.5
rpsA 1833955 c.414G>T synonymous_variant 0.5
rpsA 1833958 c.417C>T synonymous_variant 0.5
rpsA 1833959 p.Leu140Val missense_variant 0.5
rpsA 1833970 c.429G>C synonymous_variant 0.75
rpsA 1833976 c.435C>T synonymous_variant 0.75
rpsA 1833979 c.438T>C synonymous_variant 0.75
rpsA 1833985 c.444G>T synonymous_variant 0.75
rpsA 1833994 c.453G>C synonymous_variant 0.75
rpsA 1833997 c.456G>T synonymous_variant 0.75
rpsA 1834000 c.459G>T synonymous_variant 0.6
rpsA 1834012 c.471G>A synonymous_variant 0.6
rpsA 1834015 c.474G>C synonymous_variant 0.5
rpsA 1834018 c.477C>T synonymous_variant 0.5
rpsA 1834024 c.483G>C synonymous_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918327 p.Val130Phe missense_variant 0.29
tlyA 1918742 p.Pro268Leu missense_variant 0.17
PPE35 2168465 c.2147delT frameshift_variant 0.33
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168795 c.1818G>T synonymous_variant 0.33
Rv1979c 2223205 c.-41A>C upstream_gene_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726546 c.354C>A synonymous_variant 0.2
ribD 2986990 p.Gly51Val missense_variant 0.2
ribD 2987483 c.645C>T synonymous_variant 0.4
Rv2752c 3065507 p.Ala229Thr missense_variant 0.18
Rv2752c 3066363 c.-172G>A upstream_gene_variant 0.33
thyX 3068007 c.-62G>T upstream_gene_variant 0.67
thyA 3073855 p.Cys206Phe missense_variant 0.67
thyA 3074221 c.250delG frameshift_variant 0.15
ald 3086644 c.-176G>A upstream_gene_variant 0.4
Rv3083 3448366 c.-138C>A upstream_gene_variant 0.33
fprA 3474294 c.288C>T synonymous_variant 0.22
fprA 3475179 p.Glu391Asp missense_variant 0.67
fbiA 3640579 p.Ala13Thr missense_variant 0.5
fbiA 3640711 p.Arg57Ser missense_variant 0.33
fbiB 3641349 c.-186G>T upstream_gene_variant 0.5
fbiB 3641847 p.Ala105Ser missense_variant 0.4
fbiB 3642263 c.729C>A synonymous_variant 0.4
alr 3841071 p.Gly117Val missense_variant 0.18
clpC1 4040803 c.-99G>A upstream_gene_variant 0.12
embC 4241756 p.Leu632Met missense_variant 0.14
embC 4242371 p.Ala837Thr missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244009 c.777G>T synonymous_variant 0.29
embA 4244548 p.Ile439Asn missense_variant 0.25
embB 4246767 p.Cys85Phe missense_variant 0.18
embB 4248402 p.Ala630Val missense_variant 0.25
embB 4248448 c.1935C>A synonymous_variant 0.18
aftB 4267765 p.Pro358Thr missense_variant 0.33
ethR 4327587 p.Arg13Ser missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0