TB-Profiler result

Run: SRR1791725
Summary

Run ID: SRR1791725

Sample name:

Date: 03-04-2023 18:25:59

Number of reads: 1867134

Percentage reads mapped: 92.83

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 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 0.95
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 763058 c.-312C>G upstream_gene_variant 0.12
rpoC 763226 c.-144A>G upstream_gene_variant 0.13
rpoC 763238 c.-132T>C upstream_gene_variant 0.12
rpoC 764293 c.924G>C synonymous_variant 0.13
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 1304559 p.Glu543Asp missense_variant 0.27
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471985 n.140T>C non_coding_transcript_exon_variant 0.13
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.13
rrs 1472029 n.184C>T non_coding_transcript_exon_variant 0.17
rrs 1472041 n.196C>T non_coding_transcript_exon_variant 0.17
rrs 1472042 n.197T>C non_coding_transcript_exon_variant 0.18
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.18
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.18
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.18
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.16
rrs 1472438 n.593T>C non_coding_transcript_exon_variant 0.18
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.19
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.19
rrs 1472456 n.611T>C non_coding_transcript_exon_variant 0.19
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.19
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.19
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.19
rrs 1472683 n.838_839insTA non_coding_transcript_exon_variant 0.15
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.12
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.14
rrs 1473111 n.1266A>T non_coding_transcript_exon_variant 0.14
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.13
rrl 1474710 n.1053T>G non_coding_transcript_exon_variant 0.16
rrl 1474711 n.1054G>T non_coding_transcript_exon_variant 0.16
rrl 1474713 n.1056T>A non_coding_transcript_exon_variant 0.16
rrl 1474715 n.1058_1059insC non_coding_transcript_exon_variant 0.17
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.15
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.16
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.14
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.13
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.12
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.14
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.16
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.13
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.19
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.15
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.15
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.16
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.16
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.17
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.17
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.17
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.17
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.17
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.18
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.15
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.15
rrl 1476103 n.2446C>A non_coding_transcript_exon_variant 0.15
rrl 1476108 n.2451T>G non_coding_transcript_exon_variant 0.15
rrl 1476110 n.2453G>T non_coding_transcript_exon_variant 0.15
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.18
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.18
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.17
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.17
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.19
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.16
rrl 1476246 n.2589G>A non_coding_transcript_exon_variant 0.16
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.16
rrl 1476256 n.2599A>C non_coding_transcript_exon_variant 0.18
rrl 1476262 n.2605G>A non_coding_transcript_exon_variant 0.19
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.19
rrl 1476529 n.2872A>T non_coding_transcript_exon_variant 0.18
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.13
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.12
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.12
rpsA 1834261 c.720A>G synonymous_variant 0.12
rpsA 1834264 c.723G>C synonymous_variant 0.13
rpsA 1834297 c.756C>T synonymous_variant 0.13
rpsA 1834303 c.762T>G synonymous_variant 0.13
rpsA 1834306 c.765T>C synonymous_variant 0.13
rpsA 1834348 c.807T>C synonymous_variant 0.14
rpsA 1834366 c.825A>G synonymous_variant 0.14
rpsA 1834375 c.834G>C synonymous_variant 0.13
rpsA 1834378 c.837T>C synonymous_variant 0.13
rpsA 1834420 c.879C>T synonymous_variant 0.12
rpsA 1834423 c.882G>C synonymous_variant 0.12
rpsA 1834451 c.910T>C synonymous_variant 0.13
rpsA 1834456 c.915T>G synonymous_variant 0.13
rpsA 1834465 c.924T>C synonymous_variant 0.12
rpsA 1834468 c.927A>G synonymous_variant 0.12
rpsA 1834489 c.948T>C synonymous_variant 0.12
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
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 2518636 c.522C>T synonymous_variant 0.13
kasA 2518642 c.528A>G synonymous_variant 0.13
kasA 2518651 c.537C>G synonymous_variant 0.12
kasA 2518672 c.558G>C synonymous_variant 0.13
kasA 2518684 c.570C>G synonymous_variant 0.13
kasA 2518688 p.Val192Phe missense_variant 0.13
kasA 2518696 c.582C>G synonymous_variant 0.13
kasA 2518705 c.591T>G synonymous_variant 0.15
kasA 2518714 c.600A>C synonymous_variant 0.14
kasA 2518715 p.Pro201Gly missense_variant 0.14
kasA 2518739 p.Ala209Thr missense_variant 0.14
kasA 2518747 c.633C>G synonymous_variant 0.12
eis 2715125 p.Thr70Ala missense_variant 1.0
folC 2747226 c.373C>A synonymous_variant 0.41
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
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
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0