TB-Profiler result

Run: ERR2653138
Summary

Run ID: ERR2653138

Sample name:

Date: 31-03-2023 22:34:39

Number of reads: 5454372

Percentage reads mapped: 34.69

Strain: lineage4.1.2.1

Drug-resistance: MDR-TB

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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288988 p.Leu85Pro missense_variant 0.95 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4407929 p.Glu92* stop_gained 0.85 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.95
mshA 575679 p.Asn111Ser missense_variant 0.99
rpoB 760115 c.309C>T synonymous_variant 0.97
rpoC 764846 c.1479_1481dupGCA disruptive_inframe_insertion 0.82
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
Rv1258c 1407489 c.-149G>A upstream_gene_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472505 n.660G>A non_coding_transcript_exon_variant 0.12
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.19
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.34
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.34
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.39
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.4
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.4
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.4
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.4
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.44
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.45
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.45
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.45
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.44
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.46
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.45
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.54
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.47
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.44
rrs 1472659 n.814G>A non_coding_transcript_exon_variant 0.44
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.44
rrs 1472669 n.824_825insTAG non_coding_transcript_exon_variant 0.43
rrs 1472677 n.832C>G non_coding_transcript_exon_variant 0.42
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.42
rrs 1472679 n.834_835insAC non_coding_transcript_exon_variant 0.42
rrs 1472684 n.841_846delGATCCG non_coding_transcript_exon_variant 0.42
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.4
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.39
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.39
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.38
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.38
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.38
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.42
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.43
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.43
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.33
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.13
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.33
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.33
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.33
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.38
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.44
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.48
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.49
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.5
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.5
rrl 1474830 n.1173A>C non_coding_transcript_exon_variant 0.5
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.51
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.51
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.53
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.53
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.5
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.45
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.45
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.38
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.32
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.13
rrl 1475692 n.2035G>A non_coding_transcript_exon_variant 0.14
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.14
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.14
rrl 1475707 n.2050T>C non_coding_transcript_exon_variant 0.14
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.13
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.1
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.18
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.24
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.44
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.47
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.48
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.5
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.5
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.5
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.5
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.5
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.5
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.49
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.49
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.5
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.5
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.52
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.67
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.7
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.76
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.78
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.81
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.81
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.81
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.81
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.82
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.82
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.85
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.85
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.8
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.77
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.77
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.76
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.75
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.75
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.76
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.75
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.75
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.75
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.75
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.75
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.74
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.7
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.67
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.62
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.5
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.34
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.21
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.21
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153936 p.Ala726Thr missense_variant 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.98
Rv2752c 3066299 c.-108C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0