TB-Profiler result

Run: ERR4769480
Summary

Run ID: ERR4769480

Sample name:

Date: 01-04-2023 06:42:16

Number of reads: 2692385

Percentage reads mapped: 88.04

Strain: La1.3

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
La1.3 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 1472644 n.799C>T non_coding_transcript_exon_variant 0.19 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.17 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 0.98
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 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.11
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.14
rrs 1472474 n.629C>T non_coding_transcript_exon_variant 0.98
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.12
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.11
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.16
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.18
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.18
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.17
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.23
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.15
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.22
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.22
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.17
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.11
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.11
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.11
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.16
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.14
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.15
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.17
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.14
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.15
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.14
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.15
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.14
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.14
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.13
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.14
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.13
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.14
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.13
rrs 1473127 n.1282G>A non_coding_transcript_exon_variant 0.12
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.18
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.17
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.17
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.17
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.15
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.15
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.15
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.12
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.12
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.12
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.12
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.12
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.13
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.12
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.1
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.14
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.24
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.25
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.21
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.21
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.23
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.11
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.23
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.29
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.27
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.26
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.26
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.26
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.27
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.25
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.25
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.25
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.27
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.27
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.25
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.3
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.37
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.37
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.38
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.36
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.36
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.24
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.22
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.34
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.22
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.33
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.17
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.12
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.11
rrl 1476728 n.3071T>C non_coding_transcript_exon_variant 1.0
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 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
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 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 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
embC 4241384 p.Pro508Thr 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 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249640 c.3127T>C synonymous_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