TB-Profiler result

Run: ERR176517
Summary

Run ID: ERR176517

Sample name:

Date: 31-03-2023 15:03:55

Number of reads: 2076407

Percentage reads mapped: 56.37

Strain: lineage1.1.3.2

Drug-resistance: Sensitive

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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 0.98
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 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
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 6952 c.-350C>T upstream_gene_variant 1.0
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 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.98
ccsA 619695 c.-196G>A upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.96
rpoC 763886 c.517C>A synonymous_variant 0.96
rpoC 765171 p.Pro601Leu missense_variant 0.98
rpoC 765230 p.Ala621Thr missense_variant 0.98
rpoC 765835 c.2466C>G 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
rplC 801166 p.Gly120Ser missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.27
rrs 1472128 n.283G>T non_coding_transcript_exon_variant 0.27
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.29
rrs 1472138 n.293C>A non_coding_transcript_exon_variant 0.29
rrs 1472147 n.302G>T non_coding_transcript_exon_variant 0.29
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.31
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.31
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.39
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.39
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.29
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.29
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.29
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.29
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.18
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.18
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.14
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.13
rrs 1472263 n.418C>T non_coding_transcript_exon_variant 0.13
rrs 1472269 n.424G>A non_coding_transcript_exon_variant 0.15
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.19
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.33
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 0.37
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.48
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.51
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.5
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>G non_coding_transcript_exon_variant 0.51
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.51
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.53
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.47
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.31
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.14
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.12
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.27
rrs 1472719 n.874G>A non_coding_transcript_exon_variant 0.3
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.47
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.48
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.54
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.55
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.54
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.56
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.52
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.15
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.15
rrs 1473189 n.1344C>G non_coding_transcript_exon_variant 0.16
rrs 1473194 n.1349A>G non_coding_transcript_exon_variant 0.18
rrs 1473208 n.1363G>C non_coding_transcript_exon_variant 0.18
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.12
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.12
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.12
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.12
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.12
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.11
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.11
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.1
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.1
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.5
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.6
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.7
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.74
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.77
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 0.86
rrl 1476420 n.2763G>A non_coding_transcript_exon_variant 0.85
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.84
rrl 1476433 n.2776C>T non_coding_transcript_exon_variant 0.83
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.78
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.73
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.71
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.59
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.44
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.19
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.13
inhA 1674883 p.Ile228Val missense_variant 1.0
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 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.25
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339153 p.Leu12Phe missense_variant 0.21
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449628 c.1125T>C synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3642173 c.639G>A synonymous_variant 1.0
fbiB 3642780 p.Val416Ile missense_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.16
rpoA 3878687 c.-180A>C upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.27
clpC1 4040517 p.Val63Ala missense_variant 0.95
embC 4239842 c.-21C>A upstream_gene_variant 0.23
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242422 p.Trp854Gly missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245266 c.2034C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
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