TB-Profiler result

Run: ERR4819867
Summary

Run ID: ERR4819867

Sample name:

Date: 01-04-2023 16:20:59

Number of reads: 361207

Percentage reads mapped: 81.1

Strain: lineage1.1.3.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.2 Indo-Oceanic NA RD239 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 1472733 n.888G>A non_coding_transcript_exon_variant 0.97 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
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6343 c.-959G>A upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8188 p.Leu296Pro missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8991 p.His564Tyr missense_variant 0.25
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9194 c.1893G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9790 p.Ala830Val missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.21
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619695 c.-196G>A upstream_gene_variant 1.0
rpoB 759615 c.-192A>C upstream_gene_variant 0.33
rpoB 760030 p.Asn75Thr missense_variant 0.22
rpoB 760241 c.435G>T synonymous_variant 0.12
rpoB 762411 p.Gln869* stop_gained 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764457 p.Pro363Leu missense_variant 0.17
rpoC 764828 p.Leu487Phe missense_variant 0.2
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 766864 c.3495G>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.15
mmpL5 777122 c.1359C>T synonymous_variant 0.15
mmpL5 777128 c.1353A>G synonymous_variant 0.14
mmpL5 777150 p.Asn444Ser missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302734 c.-197A>T upstream_gene_variant 0.18
Rv1258c 1406662 p.Thr227Pro missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.5
rrs 1472078 n.233C>T non_coding_transcript_exon_variant 0.5
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.5
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.5
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.5
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.5
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.67
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.67
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.5
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.67
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.67
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.67
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.89
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.9
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.9
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.92
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.94
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.44
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.96
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.96
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 1.0
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 1.0
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 1.0
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.97
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 1.0
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.97
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 1.0
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.94
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.97
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.97
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.94
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.94
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.88
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.67
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.67
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.5
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.6
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.33
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.33
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.33
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.29
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.22
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.22
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.22
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.4
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.4
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.4
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.5
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 1.0
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 1.0
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 1.0
rpsA 1833455 c.-87A>T upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918535 p.His199Pro missense_variant 0.18
ndh 2103225 c.-183A>C upstream_gene_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2221793 p.Val458Met missense_variant 0.14
Rv1979c 2222300 p.Val289Leu missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222317 p.Ala283Val missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518937 p.Phe275Leu missense_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 0.95
ahpC 2726157 c.-36C>A upstream_gene_variant 0.18
folC 2747589 p.Thr4Ala missense_variant 0.2
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3067134 c.-943C>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339246 c.129C>T synonymous_variant 0.29
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449723 p.Cys407Phe missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474215 p.Thr70Met missense_variant 0.22
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612223 c.894C>A synonymous_variant 0.22
fbiA 3640386 c.-157A>G upstream_gene_variant 0.15
fbiB 3641692 p.Val53Ala missense_variant 0.17
fbiB 3642173 c.639G>A synonymous_variant 1.0
rpoA 3878687 c.-180A>C upstream_gene_variant 1.0
ddn 3986731 c.-113A>G upstream_gene_variant 0.22
clpC1 4038832 p.Asp625Asn missense_variant 0.29
clpC1 4040314 p.Leu131Met missense_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241832 p.Trp657* stop_gained 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243696 p.Ile155Arg missense_variant 0.18
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247016 p.Ser168Leu missense_variant 0.13
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267538 c.1299G>A synonymous_variant 0.14
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326365 p.Lys370Thr missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
embR 1415601 c.-1065_*579del transcript_ablation 1.0