TB-Profiler result

Run: ERR2229204
Summary

Run ID: ERR2229204

Sample name:

Date: 31-03-2023 16:48:58

Number of reads: 1192402

Percentage reads mapped: 97.39

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 0.2 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.16 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 7362 p.Glu21Gln missense_variant 1.0
mshA 575361 p.Arg5Gln missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.3
rpoC 763534 c.165T>C synonymous_variant 0.15
rpoC 763537 c.168C>G synonymous_variant 0.14
rpoC 764087 p.Leu240Ile missense_variant 0.14
rpoC 764293 c.924G>T synonymous_variant 0.12
rpoC 764334 p.Pro322Gln missense_variant 0.15
rpoC 765817 c.2448G>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776249 c.2232A>G synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801117 c.309G>T synonymous_variant 0.15
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.17
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.18
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.19
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.19
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.12
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.17
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.16
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.24
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.2
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.11
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.12
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.12
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.15
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.25
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.19
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.18
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.18
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.11
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.11
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.11
rrl 1473862 n.205C>T non_coding_transcript_exon_variant 0.21
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.15
rrl 1473887 n.230T>G non_coding_transcript_exon_variant 0.17
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.13
rrl 1473899 n.242A>G non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.13
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.16
rrl 1474202 n.545T>G non_coding_transcript_exon_variant 0.18
rrl 1474218 n.561T>G non_coding_transcript_exon_variant 0.16
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.15
rrl 1474265 n.608G>T non_coding_transcript_exon_variant 0.12
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.12
rrl 1474271 n.614A>G non_coding_transcript_exon_variant 0.11
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.11
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.19
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.18
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.22
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.14
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.19
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.11
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.15
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.37
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.28
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.28
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.23
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.34
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.21
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.18
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.27
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.35
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.39
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.36
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.15
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.15
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.12
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.15
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.17
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.15
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.15
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.21
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.19
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.19
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.19
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.22
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.21
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.13
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.26
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.14
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.14
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.19
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.14
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.17
fabG1 1673346 c.-94C>G upstream_gene_variant 0.15
fabG1 1673349 c.-91G>C upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102287 c.756C>A synonymous_variant 0.14
katG 2154632 p.Gly494Cys missense_variant 0.13
PPE35 2167918 p.Phe899Leu missense_variant 0.11
PPE35 2168047 p.Leu856Val missense_variant 0.14
PPE35 2168051 p.Val854Ile missense_variant 0.14
PPE35 2168140 p.Ala825Thr missense_variant 0.22
PPE35 2168143 p.Phe824Leu missense_variant 0.2
PPE35 2168150 c.2463T>C synonymous_variant 0.17
PPE35 2168184 p.Thr810Met missense_variant 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169717 p.Asn299Ile missense_variant 0.24
PPE35 2169725 c.888T>C synonymous_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.35
PPE35 2170053 p.Thr187Ser missense_variant 0.32
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518567 c.453G>T synonymous_variant 0.18
pepQ 2860104 c.315C>T synonymous_variant 0.13
Rv2752c 3064908 p.Ser428Arg missense_variant 0.29
Rv3083 3448400 c.-104G>T upstream_gene_variant 0.13
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3612423 p.Val232Leu missense_variant 0.22
Rv3236c 3612635 p.Ala161Glu missense_variant 0.17
Rv3236c 3613005 p.Leu38Met missense_variant 0.12
Rv3236c 3613142 c.-26A>G upstream_gene_variant 0.11
fbiA 3641499 p.Met319Ile missense_variant 0.15
fbiB 3641936 c.402C>A synonymous_variant 0.21
fbiB 3642047 c.513G>C synonymous_variant 0.13
alr 3841235 p.Met62Ile missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.17
clpC1 4039602 p.Ala368Val missense_variant 0.13
clpC1 4040324 c.381G>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244477 c.1245G>T synonymous_variant 0.15
embB 4246544 p.Thr11Pro missense_variant 0.11
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
ethR 4327958 p.Leu137Pro missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0