TB-Profiler result

Run: ERR1213875
Summary

Run ID: ERR1213875

Sample name:

Date: 31-03-2023 12:42:52

Number of reads: 8178800

Percentage reads mapped: 98.22

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.98
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.92
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 1472307 n.462C>T non_coding_transcript_exon_variant 0.43 streptomycin
thyX 3067961 c.-16C>T upstream_gene_variant 0.12 para-aminosalicylic_acid
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 8040 p.Gly247Ser missense_variant 0.92
gyrA 8966 c.1665C>T synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576577 c.1230C>A synonymous_variant 0.18
ccsA 619697 c.-194A>T upstream_gene_variant 0.25
ccsA 619812 c.-79C>A upstream_gene_variant 0.12
rpoB 762841 p.Pro1012Leu missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766953 p.Ala1195Val missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776110 p.Met791Val missense_variant 0.1
mmpL5 776111 p.Ile790Met missense_variant 0.1
mmpL5 776942 c.1539A>G synonymous_variant 0.11
mmpL5 777568 p.Gly305Ser missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303383 c.453G>C synonymous_variant 0.12
embR 1417184 p.Leu55Pro missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471969 n.124T>C non_coding_transcript_exon_variant 0.81
rrs 1472035 n.190G>T non_coding_transcript_exon_variant 0.76
rrs 1472042 n.197T>C non_coding_transcript_exon_variant 0.74
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.74
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.73
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.78
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.74
rrs 1472300 n.455C>T non_coding_transcript_exon_variant 0.46
rrs 1473091 n.1246G>T non_coding_transcript_exon_variant 0.13
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.85
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.94
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.98
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.99
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.98
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.91
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.92
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.92
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.93
rrl 1473924 n.267_268insT non_coding_transcript_exon_variant 0.93
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.94
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.92
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.9
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.91
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.83
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.86
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.86
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.87
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.9
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.89
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.95
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.96
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.95
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.87
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.83
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.85
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.76
rrl 1474374 n.717T>A non_coding_transcript_exon_variant 0.61
rrl 1474447 n.790G>A non_coding_transcript_exon_variant 0.6
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.83
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.84
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.85
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.87
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.94
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.99
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.99
rrl 1475005 n.1348C>T non_coding_transcript_exon_variant 0.82
rrl 1475006 n.1349A>G non_coding_transcript_exon_variant 0.82
rrl 1475013 n.1356G>A non_coding_transcript_exon_variant 0.83
rrl 1475028 n.1371G>A non_coding_transcript_exon_variant 0.9
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.93
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.76
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.74
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.62
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.59
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.68
rrl 1475289 n.1632G>A non_coding_transcript_exon_variant 0.69
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.69
rrl 1475297 n.1640C>T non_coding_transcript_exon_variant 0.74
rrl 1475315 n.1658A>C non_coding_transcript_exon_variant 0.71
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.73
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.8
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.86
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.85
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.87
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.85
rrl 1475446 n.1789G>C non_coding_transcript_exon_variant 0.82
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.76
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.65
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.56
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.59
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.64
rrl 1475760 n.2103C>T non_coding_transcript_exon_variant 0.21
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.22
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.44
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.52
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.52
rrl 1476032 n.2375C>T non_coding_transcript_exon_variant 0.46
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.46
rrl 1476035 n.2378G>A non_coding_transcript_exon_variant 0.46
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.62
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.61
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.66
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.67
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.69
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.74
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.74
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.75
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.58
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.53
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.5
rrl 1476314 n.2657T>A non_coding_transcript_exon_variant 0.12
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.71
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.71
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.82
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.83
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.74
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.68
rrl 1476746 n.3089T>A non_coding_transcript_exon_variant 0.52
rrl 1476755 n.3098G>T non_coding_transcript_exon_variant 0.53
rrl 1476759 n.3102T>A non_coding_transcript_exon_variant 0.5
rrl 1476770 n.3113T>C non_coding_transcript_exon_variant 0.46
rrl 1476771 n.3114G>A non_coding_transcript_exon_variant 0.46
rpsA 1834836 p.Met432Thr missense_variant 0.92
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918190 p.Arg84Leu missense_variant 0.25
ndh 2101968 p.Arg359Ser missense_variant 0.31
katG 2154036 c.2076C>T synonymous_variant 0.14
katG 2154213 c.1899C>T synonymous_variant 0.11
katG 2155857 c.255C>T synonymous_variant 0.2
katG 2156196 c.-85C>T upstream_gene_variant 0.97
PPE35 2169320 p.Leu431Phe missense_variant 0.29
Rv1979c 2222325 p.Asn280Lys missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290237 c.-996G>A upstream_gene_variant 0.12
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714357 p.Gly326Cys missense_variant 0.13
folC 2746340 p.Ala420Val missense_variant 1.0
pepQ 2859781 p.Gln213Arg missense_variant 0.12
pepQ 2859929 p.Arg164Gly missense_variant 0.22
pepQ 2859944 p.Ala159Thr missense_variant 0.2
Rv2752c 3064771 p.Ala474Val missense_variant 0.15
thyX 3067437 p.Ala170Val missense_variant 0.22
thyX 3067515 p.Ser144Ile missense_variant 0.29
thyA 3073868 p.Thr202Ala missense_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339750 c.633C>T synonymous_variant 0.2
Rv3083 3449947 p.Val482Leu missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474854 p.Lys283Thr missense_variant 0.11
fprA 3475312 p.Pro436Ser missense_variant 0.13
Rv3236c 3613242 c.-126G>A upstream_gene_variant 0.12
alr 3840440 c.981G>A synonymous_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.5
clpC1 4039488 p.Ala406Val missense_variant 0.14
clpC1 4040447 c.257delA frameshift_variant 0.12
embC 4240346 p.Asp162Asn missense_variant 0.18
embC 4241218 c.1356G>A synonymous_variant 0.14
embC 4241410 c.1548C>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243303 p.Gly24Asp missense_variant 0.12
embA 4243533 p.Gly101Ser missense_variant 0.15
embB 4249417 c.2904A>G synonymous_variant 0.11
embB 4249432 c.2919A>G synonymous_variant 0.12
embB 4249433 c.2920C>T synonymous_variant 0.12
embB 4249441 c.2928A>G synonymous_variant 0.11
embB 4249444 c.2931T>C synonymous_variant 0.12
embB 4249447 c.2934G>C synonymous_variant 0.11
embB 4249450 c.2937C>T synonymous_variant 0.12
embB 4249459 c.2946G>A synonymous_variant 0.13
aftB 4267445 c.1392G>A synonymous_variant 0.14
aftB 4267811 c.1026G>A synonymous_variant 0.17
aftB 4267860 p.Trp326* stop_gained 0.15
aftB 4268310 p.Ala176Val missense_variant 0.18
aftB 4268424 p.Gly138Val missense_variant 0.2
whiB6 4338265 p.Arg86Gln missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0