TB-Profiler result

Run: ERR4819080
Summary

Run ID: ERR4819080

Sample name:

Date: 01-04-2023 15:54:53

Number of reads: 1064085

Percentage reads mapped: 93.01

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 0.97
lineage4.1.2 Euro-American T;H None 0.96
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.96
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 1472644 n.799C>T non_coding_transcript_exon_variant 0.62 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.22 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.12 kanamycin, capreomycin, aminoglycosides, amikacin
gid 4408100 c.102delG frameshift_variant 0.94 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 0.94
mshA 575679 p.Asn111Ser missense_variant 0.85
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761152 p.Leu449Gln missense_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765773 p.Ile802Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776083 p.Ala800Ser missense_variant 0.96
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.32
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.41
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.44
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.5
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.29
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.43
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.29
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.43
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.29
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.25
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 1.0
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.83
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.71
rrs 1472674 n.829T>G non_coding_transcript_exon_variant 0.71
rrs 1472675 n.830T>A non_coding_transcript_exon_variant 0.71
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.71
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.71
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.22
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.56
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.22
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.2
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.2
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.36
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.18
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.29
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.4
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.4
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.4
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.61
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.7
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.7
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.7
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.7
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.71
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.7
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.7
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.7
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.79
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.62
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.65
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.57
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.27
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.19
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.13
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.13
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.13
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.12
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.12
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.12
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.13
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.22
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.17
rrs 1473254 n.1409A>G non_coding_transcript_exon_variant 0.12
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.12
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.33
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.38
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.38
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.38
rrl 1475757 n.2101_2104delACCC non_coding_transcript_exon_variant 0.33
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.43
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.43
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.25
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.22
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.22
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.25
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.22
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.22
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.22
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.22
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.19
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.19
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.17
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.1
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.2
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.27
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.5
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.53
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.47
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.35
rrl 1476482 n.2825A>G non_coding_transcript_exon_variant 0.12
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.21
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.19
inhA 1674718 p.Arg173Gly missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170466 c.147A>G synonymous_variant 0.11
PPE35 2170469 c.144G>C synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.98
thyX 3067299 p.Leu216Pro missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448343 c.-161C>T upstream_gene_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4040087 c.618G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.1
embB 4246555 c.42G>C synonymous_variant 0.16
embB 4246556 p.Ala15Pro missense_variant 0.16
embB 4246563 p.Leu17Trp missense_variant 0.16
embB 4246567 c.54G>T synonymous_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0