TB-Profiler result

Run: SRR5382721
Summary

Run ID: SRR5382721

Sample name:

Date: 04-04-2023 10:23:43

Number of reads: 4673170

Percentage reads mapped: 68.03

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
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 0.99
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.29
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.39
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.37
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.38
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.44
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.35
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.27
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.17
rrs 1472349 n.504A>T non_coding_transcript_exon_variant 0.14
rrs 1472374 n.529T>A non_coding_transcript_exon_variant 0.14
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.17
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.18
rrs 1472390 n.545T>C non_coding_transcript_exon_variant 0.2
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.22
rrs 1472398 n.553T>C non_coding_transcript_exon_variant 0.25
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.3
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.3
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.3
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.25
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.33
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.33
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.33
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.73
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.73
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.73
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.8
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.64
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.46
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.43
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.36
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.46
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.39
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.44
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.44
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.5
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.5
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.44
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.4
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.38
rrl 1474825 n.1168G>A non_coding_transcript_exon_variant 0.4
rrl 1474828 n.1171G>C non_coding_transcript_exon_variant 0.4
rrl 1474832 n.1176delG non_coding_transcript_exon_variant 0.4
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.22
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.22
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.18
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.15
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.15
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.2
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.24
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.6
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.67
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.67
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.67
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.67
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.83
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.83
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.83
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.82
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.82
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.75
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.75
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.69
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.56
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.56
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.56
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.23
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
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 2170048 p.Leu189Val missense_variant 0.19
PPE35 2170053 p.Thr187Ser missense_variant 0.19
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517917 c.-198G>A upstream_gene_variant 1.0
kasA 2518132 c.18C>T 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
fbiB 3641590 p.Gly19Glu missense_variant 0.98
rpoA 3878630 c.-124delC upstream_gene_variant 0.9
clpC1 4038403 c.2302T>C synonymous_variant 0.98
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 0.97
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.98
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