TB-Profiler result

Run: ERR6209443
Summary

Run ID: ERR6209443

Sample name:

Date: 02-04-2023 01:57:07

Number of reads: 5864162

Percentage reads mapped: 91.53

Strain: La1.2

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
La1 M.bovis None None 1.0
La1.2 M.bovis None 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 0.36 streptomycin
pncA 2289073 p.His57Asp missense_variant 1.0 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 5752 c.513G>A synonymous_variant 1.0
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7821 c.520C>T synonymous_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 8741 c.1440C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 0.99
mshA 576108 p.Ala254Gly missense_variant 0.27
mshA 576482 p.Val379Leu missense_variant 0.17
rpoC 762803 c.-567C>T upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1406663 c.678C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.14
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.14
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 0.14
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.14
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.19
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.2
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.2
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.23
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.23
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.25
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.24
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.23
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.22
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.23
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.23
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.21
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.21
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.2
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.24
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.23
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.25
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.24
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.24
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.25
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.27
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.27
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.28
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.28
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.26
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.26
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.25
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.27
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.33
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.35
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.37
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.3
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.28
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.28
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.3
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.29
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.29
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.31
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.31
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.34
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.33
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.23
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.11
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.14
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.14
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.14
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.12
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.12
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.14
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.36
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.39
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.49
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.51
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.51
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.5
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.51
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.47
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.48
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.47
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.47
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.47
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.46
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.46
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.46
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.47
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.48
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.57
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.64
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.66
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.65
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.65
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.61
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.62
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.6
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.57
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.56
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.57
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.62
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.57
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.45
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.39
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.36
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.37
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.36
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.36
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.36
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.37
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.37
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.36
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.35
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.35
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.37
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.35
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.34
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.26
rpsA 1833422 c.-120G>T upstream_gene_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102106 p.Gly313Arg missense_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 0.99
katG 2156025 c.87C>A synonymous_variant 1.0
katG 2156465 c.-354C>T upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 0.99
PPE35 2170065 p.Ala183Gly missense_variant 0.16
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
pepQ 2860159 p.Ala87Gly missense_variant 0.16
thyX 3067786 p.Thr54Ala missense_variant 1.0
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
fbiD 3339154 p.Ile13Leu missense_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.28
Rv3083 3448745 p.Ile81Ser missense_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.27
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247173 c.660G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
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 1.0