TB-Profiler result

Run: ERR3324355
Summary

Run ID: ERR3324355

Sample name:

Date: 01-04-2023 01:50:26

Number of reads: 1321670

Percentage reads mapped: 84.09

Strain: lineage4.1.1.3

Drug-resistance: HR-TB

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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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
katG 2153982 c.2129delT frameshift_variant 0.11 isoniazid
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 7758 p.Ile153Leu missense_variant 0.12
gyrA 8124 p.Pro275Ser missense_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760208 c.404dupA frameshift_variant 0.11
rpoB 761054 c.1248G>A synonymous_variant 0.17
rpoC 763728 p.Leu120Pro missense_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767095 p.Ser1242Arg missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775795 p.Ala896Thr missense_variant 0.11
mmpL5 775915 p.Ala856Thr missense_variant 0.14
mmpL5 775936 p.Asp849His missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.15
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.15
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.25
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.25
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.28
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.3
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.37
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.37
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.41
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.28
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.12
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.26
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.25
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.25
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.19
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.18
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.14
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.14
rrs 1472669 n.824_825insTAGA non_coding_transcript_exon_variant 0.19
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.19
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.19
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.18
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.18
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.18
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.17
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.17
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.3
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.41
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.44
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.56
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.56
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.37
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.38
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.1
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.17
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.14
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.16
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.16
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.14
rrs 1473080 n.1235C>A non_coding_transcript_exon_variant 0.13
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.1
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.1
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.15
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.14
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.13
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.14
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.1
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.14
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.2
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.24
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.1
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.3
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.33
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.28
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.28
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.28
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.28
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.28
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.28
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.13
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.12
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.11
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.11
rrl 1475835 n.2178T>A non_coding_transcript_exon_variant 0.12
rrl 1475905 n.2248G>A non_coding_transcript_exon_variant 0.12
rrl 1475925 n.2268A>G non_coding_transcript_exon_variant 0.12
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.23
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.3
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.3
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.72
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.78
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.77
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.72
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.7
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.7
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.7
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.7
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.7
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.7
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.62
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.62
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.62
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.6
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.59
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.55
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.51
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.53
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.53
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.57
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.54
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.54
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.54
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.45
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.44
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.37
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.21
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.21
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.21
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.2
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.2
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.18
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.17
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.17
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.23
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.21
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.37
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.37
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.38
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.37
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.28
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.18
rrl 1476627 n.2971T>A non_coding_transcript_exon_variant 0.11
rrl 1476637 n.2980C>G non_coding_transcript_exon_variant 0.1
rpsA 1833727 c.186G>A synonymous_variant 1.0
rpsA 1834330 c.789C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918624 p.Pro229Ser missense_variant 0.11
katG 2154282 c.1830G>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726081 c.-112C>T upstream_gene_variant 0.11
ribD 2986974 p.Ile46Val missense_variant 0.12
ribD 2986985 p.Leu49Phe missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474288 c.282C>A synonymous_variant 0.13
clpC1 4040241 p.Thr155Phe missense_variant 0.25
clpC1 4040249 p.Glu152Gly missense_variant 0.25
clpC1 4040294 p.Gln137His missense_variant 0.11
clpC1 4040522 p.Ser61Arg missense_variant 0.18
clpC1 4040733 c.-29C>A upstream_gene_variant 0.11
embC 4242496 p.Asp878Glu missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249668 p.Tyr1052Phe missense_variant 0.11
embB 4249725 p.Val1071Asp missense_variant 0.11
ubiA 4269864 c.-32delG upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0