TB-Profiler result

Run: SRR1792140
Summary

Run ID: SRR1792140

Sample name:

Date: 03-04-2023 18:45:47

Number of reads: 814860

Percentage reads mapped: 22.55

Strain: 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 1.0
La1.8 M.bovis None None 1.0
La1.8.1 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 0.69 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
gyrB 5951 p.Ala238Pro missense_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 8285 c.984C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_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 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304893 p.Gly655Arg missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.13
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.14
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.13
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.14
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.15
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.32
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.29
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.61
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.63
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.62
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.61
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.62
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.62
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.66
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.67
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.68
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.69
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.64
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.62
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.62
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.63
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.64
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.63
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.63
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.67
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.67
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.68
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.68
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.67
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.63
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.56
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.47
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.27
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.25
rrs 1472826 n.981G>A non_coding_transcript_exon_variant 0.25
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.25
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.24
rrs 1472836 n.991G>C non_coding_transcript_exon_variant 0.24
rrs 1472858 n.1013_1014insA non_coding_transcript_exon_variant 0.23
rrs 1472861 n.1016G>C non_coding_transcript_exon_variant 0.23
rrs 1472867 n.1022T>C non_coding_transcript_exon_variant 0.23
rrs 1472873 n.1028C>A non_coding_transcript_exon_variant 0.24
rrs 1472875 n.1030T>A non_coding_transcript_exon_variant 0.26
rrs 1472876 n.1031G>A non_coding_transcript_exon_variant 0.25
rrs 1472877 n.1032T>A non_coding_transcript_exon_variant 0.25
rrs 1472880 n.1035_1036insA non_coding_transcript_exon_variant 0.24
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.27
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.25
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.25
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.25
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.25
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.25
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.25
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.25
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.25
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.25
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.27
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.34
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.37
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.32
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.33
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.33
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.33
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.33
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.33
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.34
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.33
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.33
rrs 1473290 n.1445C>A non_coding_transcript_exon_variant 0.36
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.36
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.37
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.37
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.39
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.41
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.41
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.38
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.41
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.49
rrl 1476234 n.2577G>A non_coding_transcript_exon_variant 0.57
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.65
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.7
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.69
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.69
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.69
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.67
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.67
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.67
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.67
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.67
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.68
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.67
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.66
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.67
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.67
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.7
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.73
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.75
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.75
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.76
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.77
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.76
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.77
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.76
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.76
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.76
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.74
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.7
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.64
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.56
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.55
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.55
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.55
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.55
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.55
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.55
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.55
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.55
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.55
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.54
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.53
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.49
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.49
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.36
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102193 p.Arg284Trp 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 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2170255 p.Leu120Val missense_variant 0.1
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
kasA 2519161 c.1047G>A synonymous_variant 1.0
eis 2715125 p.Thr70Ala 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
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
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
embA 4244873 c.1641C>G synonymous_variant 0.12
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T 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