TB-Profiler result

Run: SRR19304096
Summary

Run ID: SRR19304096

Sample name:

Date: 03-04-2023 21:24:36

Number of reads: 6565333

Percentage reads mapped: 98.7

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
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 8741 c.1440C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491137 p.Glu119Lys missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.24
mshA 576609 p.Ala421Val missense_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
mmpL5 777574 p.Phe303Leu missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.14
rrs 1472496 n.651T>A non_coding_transcript_exon_variant 0.13
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.12
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.17
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.17
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.2
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.2
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.18
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.18
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.17
rrl 1474280 n.623C>T non_coding_transcript_exon_variant 0.15
rrl 1474281 n.624A>G non_coding_transcript_exon_variant 0.15
rrl 1474284 n.631_633delCCT non_coding_transcript_exon_variant 0.17
rrl 1474293 n.637_651delCCTCTCCGGAGGAGG non_coding_transcript_exon_variant 0.18
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.14
rrl 1474316 n.659T>C non_coding_transcript_exon_variant 0.13
rrl 1474317 n.660G>A non_coding_transcript_exon_variant 0.13
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.12
rrl 1474351 n.694G>T non_coding_transcript_exon_variant 0.12
rrl 1474353 n.696A>T non_coding_transcript_exon_variant 0.12
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.12
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.11
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.13
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.13
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.13
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.13
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.12
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.12
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.44
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.33
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.33
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.33
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.33
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.3
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.27
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.14
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.12
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.11
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.11
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.14
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.17
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.27
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.26
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.25
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.15
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.17
fabG1 1673296 c.-144T>C upstream_gene_variant 1.0
fabG1 1673326 c.-113delA 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 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 0.99
PPE35 2170065 p.Ala183Gly missense_variant 0.2
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 0.19
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 3339734 p.Ala206Gly missense_variant 0.68
fbiD 3339744 c.627A>C synonymous_variant 0.17
Rv3083 3448745 p.Ile81Ser missense_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 4240409 p.Pro183Ala missense_variant 0.15
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 0.22
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