TB-Profiler result

Run: ERR1815538
Summary

Run ID: ERR1815538

Sample name:

Date: 31-03-2023 15:16:04

Number of reads: 25297741

Percentage reads mapped: 90.88

Strain: La1.7.1

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
La1.7 M.bovis None None 1.0
La1.7.1 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 0.14 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.15 kanamycin, capreomycin, aminoglycosides, amikacin
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 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
rpoC 764611 c.1242G>T synonymous_variant 0.11
rpoC 764632 c.1263T>C synonymous_variant 0.11
rpoC 764635 c.1266C>G synonymous_variant 0.11
rpoC 764650 c.1281G>C synonymous_variant 0.11
rpoC 764665 c.1296C>G synonymous_variant 0.1
rpoC 764671 c.1302G>C 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 0.99
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1305445 p.Gly839Ser missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.18
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.26
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.13
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.12
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.15
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.16
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.22
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.16
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.14
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.15
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.16
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.14
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.1
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.11
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.15
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.12
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.12
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.13
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.16
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.16
rrs 1473022 n.1177G>A non_coding_transcript_exon_variant 0.18
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.18
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.21
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.17
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.18
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.17
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.16
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.16
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.15
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.15
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.11
rrl 1473871 n.214T>C non_coding_transcript_exon_variant 0.11
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.12
rrl 1473887 n.230T>A non_coding_transcript_exon_variant 0.11
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.11
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.11
rrl 1473899 n.242A>T non_coding_transcript_exon_variant 0.11
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.13
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.13
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.12
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.15
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.17
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.18
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.15
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.15
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.16
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.13
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.14
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.2
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.19
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.19
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.19
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.19
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.2
rrl 1474662 n.1005C>A non_coding_transcript_exon_variant 0.19
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.17
rrl 1474688 n.1031G>T non_coding_transcript_exon_variant 0.15
rrl 1474710 n.1053T>G non_coding_transcript_exon_variant 0.11
rrl 1474717 n.1060A>G non_coding_transcript_exon_variant 0.1
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.12
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.11
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.11
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.15
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.2
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.19
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.18
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.16
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.13
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.11
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.11
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.13
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.12
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.1
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.2
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.2
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.17
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.19
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.16
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.16
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.19
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.11
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.11
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.12
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.12
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.19
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.19
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.19
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.18
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.13
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.17
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.13
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.11
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.11
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.18
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.11
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.13
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.14
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.13
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.11
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.14
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.16
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.15
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.15
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.22
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.2
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.41
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.23
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.34
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.29
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.18
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2153933 p.Ala727Ser missense_variant 0.24
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 0.99
PPE35 2168814 c.1798dupA frameshift_variant 1.0
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
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 0.99
fbiB 3642478 p.Asp315Ala 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 0.99
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 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