TB-Profiler result

Run: ERR4818498
Summary

Run ID: ERR4818498

Sample name:

Date: 01-04-2023 15:35:37

Number of reads: 1743317

Percentage reads mapped: 98.18

Strain: lineage3.1.2.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 1.0
lineage3.1.2.1 East-African-Indian CAS2 RD750 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.12 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 7906 p.Phe202Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764551 c.1182G>C synonymous_variant 0.12
rpoC 764573 p.Leu402Ile missense_variant 0.11
rpoC 764578 c.1209C>G synonymous_variant 0.11
rpoC 764581 c.1212T>C synonymous_variant 0.11
rpoC 764582 p.Leu405Met missense_variant 0.12
rpoC 764602 c.1233C>T synonymous_variant 0.12
rpoC 764605 c.1236G>T synonymous_variant 0.11
rpoC 764611 c.1242G>T synonymous_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.11
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.11
rrs 1472100 n.259delG non_coding_transcript_exon_variant 0.12
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.3
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.3
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.3
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.3
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.3
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.44
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.35
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.4
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.13
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.29
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.22
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.18
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.42
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.36
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.36
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.36
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.36
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.4
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.58
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.53
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.12
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.5
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.12
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.14
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.14
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.36
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.17
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.17
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.33
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.1
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.1
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.25
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.23
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.24
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.25
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.17
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.13
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.18
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.15
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.15
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.15
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.15
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.15
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.15
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.15
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.14
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.23
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.12
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.12
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.27
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.33
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.35
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.28
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.28
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.2
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.26
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 0.25
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.26
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.5
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.18
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.33
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.33
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.33
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.4
rrl 1475760 n.2103C>T non_coding_transcript_exon_variant 0.4
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.4
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.4
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.4
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.4
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.4
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.4
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.6
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.62
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.46
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.45
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.47
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.33
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19
rpsA 1834294 c.753G>C synonymous_variant 0.11
rpsA 1834298 p.Gln253Glu missense_variant 0.11
rpsA 1834306 c.765T>C synonymous_variant 0.12
rpsA 1834307 p.Asp256Gln missense_variant 0.12
rpsA 1834312 c.771G>A synonymous_variant 0.12
rpsA 1834327 c.786G>T synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714401 p.Ala311Val missense_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726201 c.9G>A synonymous_variant 0.98
Rv2752c 3064750 p.Arg481His missense_variant 1.0
Rv2752c 3065005 p.Val396Gly missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethR 4327631 p.Ala28Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0