TB-Profiler result

Run: ERR4814501
Summary

Run ID: ERR4814501

Sample name:

Date: 01-04-2023 13:19:52

Number of reads: 721467

Percentage reads mapped: 96.26

Strain: lineage4.2.2.2

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 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 0.77 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 6718 c.-584C>A upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7831 p.Gly177Glu missense_variant 0.12
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
ccsA 620602 p.Pro238Thr missense_variant 0.12
ccsA 620737 p.Ser283Pro missense_variant 0.1
rpoB 759620 c.-187A>C upstream_gene_variant 0.27
rpoB 761489 c.1683G>A synonymous_variant 1.0
rpoB 762255 p.Ala817Thr missense_variant 0.17
rpoC 763259 c.-111G>T upstream_gene_variant 0.12
rpoC 763453 c.89delA frameshift_variant 0.11
rpoC 764611 c.1242G>C synonymous_variant 0.1
rpoC 765046 p.Met559Ile missense_variant 0.11
rpoC 765838 c.2469G>T synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775736 c.2745C>G synonymous_variant 0.11
mmpL5 775741 c.2740C>T synonymous_variant 0.12
mmpL5 775742 c.2739C>T synonymous_variant 0.12
mmpL5 775871 c.2610C>T synonymous_variant 0.12
mmpL5 775874 c.2607C>A synonymous_variant 0.13
mmpL5 777119 p.His454Gln missense_variant 0.13
mmpL5 777122 c.1359C>T synonymous_variant 0.15
mmpL5 777128 c.1353A>G synonymous_variant 0.19
mmpS5 778765 p.Asp47Glu missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406326 c.1015C>A synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.67
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.6
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.58
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.78
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.78
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.9
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.9
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 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.8
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.71
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.71
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.77
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.77
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.8
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.89
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.89
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.67
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.75
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.67
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.67
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.75
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.75
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.75
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.5
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.33
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.5
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.5
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.5
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.33
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.57
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.5
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.6
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 1.0
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 1.0
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 1.0
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.44
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.4
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918565 p.Leu209Pro missense_variant 0.13
tlyA 1918569 c.630G>C synonymous_variant 0.14
ndh 2102173 c.870C>T synonymous_variant 0.11
ndh 2102434 p.His203Gln missense_variant 0.15
PPE35 2167746 p.Thr956Ser missense_variant 0.11
PPE35 2170533 p.Ala27Val missense_variant 0.18
PPE35 2170540 c.73C>T synonymous_variant 0.18
Rv1979c 2222454 c.711G>C synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289744 c.-503G>A upstream_gene_variant 0.11
kasA 2519140 c.1026G>C synonymous_variant 0.17
kasA 2519143 c.1029G>C synonymous_variant 0.2
kasA 2519153 p.Ile347Val missense_variant 0.2
folC 2746257 p.Asp448Asn missense_variant 0.17
pepQ 2859625 p.Leu265Pro missense_variant 0.18
ribD 2987026 p.Ala63Val missense_variant 0.17
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 0.1
Rv3083 3449011 p.Pro170Ser missense_variant 0.15
Rv3083 3449038 p.Lys179Glu missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474307 p.Ile101Leu missense_variant 0.15
fprA 3474784 p.Pro260Thr missense_variant 0.12
Rv3236c 3612978 p.Gly47Arg missense_variant 0.14
Rv3236c 3613014 p.Val35Met missense_variant 0.12
alr 3840495 p.Leu309Pro missense_variant 0.13
rpoA 3877978 p.Lys177Met missense_variant 0.1
clpC1 4039594 p.Arg371Gly missense_variant 0.12
clpC1 4039602 p.Ala368Val missense_variant 0.12
panD 4043987 p.Arg99Ser missense_variant 0.11
embC 4241663 p.Gly601Trp missense_variant 0.18
embC 4242365 p.Ser835Pro missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247470 c.957T>C synonymous_variant 0.11
embB 4247472 p.Phe320Tyr missense_variant 0.11
embB 4247559 p.Trp349* stop_gained 0.17
embB 4247725 c.1212G>A synonymous_variant 0.12
embB 4249694 p.Trp1061Gly missense_variant 0.2
embB 4249786 c.3273G>A synonymous_variant 0.22
aftB 4268682 p.Gly52Val missense_variant 0.13
aftB 4269186 c.-350C>G upstream_gene_variant 0.12
aftB 4269633 c.-797G>A upstream_gene_variant 0.13
ethA 4326487 c.987A>C synonymous_variant 0.11
ethA 4326490 p.Asn328Asp missense_variant 0.11
ethA 4326494 p.Leu327Pro missense_variant 0.1
ethA 4326499 c.975C>T synonymous_variant 0.1
ethA 4328317 c.-844C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408088 p.Arg39Cys missense_variant 0.14