TB-Profiler result

Run: ERR4188033
Summary

Run ID: ERR4188033

Sample name:

Date: 01-04-2023 04:52:03

Number of reads: 645226

Percentage reads mapped: 53.9

Strain: lineage4;La1.8.1

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
La1 M.bovis None None 0.9
La1.8 M.bovis None None 0.87
La1.8.1 M.bovis None None 0.91
lineage4 Euro-American LAM;T;S;X;H None 0.07
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 0.25 streptomycin
pncA 2289073 p.His57Asp missense_variant 0.8 pyrazinamide
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 5079 c.-161G>A upstream_gene_variant 0.18
gyrB 5752 c.513G>A synonymous_variant 1.0
gyrA 6406 c.-896C>T upstream_gene_variant 0.88
gyrB 6446 p.Ala403Ser missense_variant 0.83
gyrA 7219 c.-83C>A upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 0.9
gyrA 8741 c.1440C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.94
gyrA 9217 p.Asp639Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.91
mshA 575654 p.Val103Met missense_variant 0.2
rpoB 762655 p.Ala950Val missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775700 c.2781G>A synonymous_variant 0.15
mmpL5 775831 p.Ala884Thr missense_variant 0.29
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
embR 1416378 c.969delC frameshift_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.33
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.25
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.2
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.2
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.2
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.2
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 0.2
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.2
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.2
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.22
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.2
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.2
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.2
rrs 1472701 n.856T>A non_coding_transcript_exon_variant 0.2
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.18
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.18
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.22
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.22
rrl 1475798 n.2141G>A non_coding_transcript_exon_variant 0.2
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.33
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.5
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.4
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.67
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.67
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.4
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.4
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.5
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.75
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.5
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.75
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.67
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.67
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.67
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.67
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.67
rrl 1476521 n.2864C>T non_coding_transcript_exon_variant 0.67
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.67
rrl 1476525 n.2868A>C non_coding_transcript_exon_variant 0.67
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.67
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.5
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.5
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.5
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.5
inhA 1674021 c.-181G>C upstream_gene_variant 0.22
rpsA 1834859 p.Ala440Thr missense_variant 0.88
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102193 p.Arg284Trp missense_variant 0.92
ndh 2103173 c.-132delG upstream_gene_variant 0.91
katG 2154724 p.Arg463Leu missense_variant 0.88
katG 2155503 c.609C>T synonymous_variant 0.86
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167861 p.Gly918Cys missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 0.75
PPE35 2168319 p.Thr765Ile missense_variant 0.86
PPE35 2168814 c.1798dupA frameshift_variant 0.91
PPE35 2168828 c.1785G>A synonymous_variant 0.17
PPE35 2169743 c.870G>C synonymous_variant 0.13
PPE35 2169748 p.Ile289Phe missense_variant 0.12
PPE35 2169754 p.Phe287Ile missense_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 0.85
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289164 c.78G>A synonymous_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 0.83
eis 2715125 p.Thr70Ala missense_variant 0.95
ribD 2987012 c.174C>T synonymous_variant 0.14
ribD 2987301 c.463C>A synonymous_variant 0.14
Rv2752c 3065329 p.Asp288Val missense_variant 0.17
ald 3086728 c.-92C>T upstream_gene_variant 0.87
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.89
Rv3083 3448783 p.Val94Ile missense_variant 0.92
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474420 c.414C>T synonymous_variant 0.22
fprA 3474427 p.Val141Ile missense_variant 0.75
fprA 3475159 p.Asn385Asp missense_variant 0.91
alr 3841193 c.228C>T synonymous_variant 0.12
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 0.89
embC 4240671 p.Thr270Ile missense_variant 0.87
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 0.94
embA 4244220 c.988C>T synonymous_variant 0.95
embB 4246551 p.Asn13Ser missense_variant 0.91
embB 4246864 c.351C>T synonymous_variant 0.93
embB 4247646 p.Glu378Ala missense_variant 0.76
embB 4248550 c.2037C>A synonymous_variant 0.12
embB 4249537 c.3024A>G synonymous_variant 0.2
aftB 4267409 c.1427delG frameshift_variant 0.17
aftB 4267491 p.Ala449Val missense_variant 0.21
aftB 4267698 p.Leu380Gln missense_variant 0.14
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_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
gid 4407588 c.615A>G synonymous_variant 0.92
gid 4407927 p.Glu92Asp missense_variant 0.18
gid 4408429 c.-227A>T upstream_gene_variant 0.13