TB-Profiler result

Run: ERR1200622
Summary

Run ID: ERR1200622

Sample name:

Date: 13-08-2022 02:32:07

Number of reads: 9925884

Percentage reads mapped: 96.15

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
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575309 c.-39C>G upstream_gene_variant 0.24
ccsA 620748 c.858T>G synonymous_variant 0.19
rpoB 761285 c.1479G>C synonymous_variant 0.24
rpoC 762836 c.-534C>G upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764725 p.Phe452Leu missense_variant 0.21
rpoC 764751 p.Val461Gly missense_variant 0.29
rpoC 765751 c.2382C>T synonymous_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
rpsL 781402 c.-158A>G upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1406750 c.591C>A synonymous_variant 0.15
embR 1417233 c.115C>T synonymous_variant 0.18
rrs 1471658 n.-188T>G upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.18
rrs 1473360 n.1515T>G non_coding_transcript_exon_variant 0.32
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.24
rrl 1476408 n.2751G>C non_coding_transcript_exon_variant 0.18
rrl 1476728 n.3071T>C non_coding_transcript_exon_variant 1.0
inhA 1674892 p.Asn231Asp missense_variant 0.22
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918069 p.Thr44Pro missense_variant 0.35
ndh 2101850 p.Val398Gly missense_variant 0.18
ndh 2102891 p.Phe51Ser missense_variant 0.14
ndh 2103147 c.-106delT upstream_gene_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 0.99
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 0.98
PPE35 2169379 p.Phe412Val 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
kasA 2518891 c.777C>A synonymous_variant 0.17
kasA 2519305 c.1191A>G synonymous_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.18
ahpC 2726756 c.564C>G synonymous_variant 0.18
Rv2752c 3064741 p.Gly484Ala missense_variant 0.18
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
ald 3087084 c.266delA frameshift_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3448929 p.Tyr142* stop_gained 0.16
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3474684 c.678T>C synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475280 p.Val425Gly missense_variant 0.23
fbiB 3641955 p.Gly141Arg missense_variant 0.2
alr 3841504 c.-84C>G upstream_gene_variant 0.15
rpoA 3877766 p.Ala248Pro missense_variant 0.2
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
ddn 3987013 p.Gly57Ala missense_variant 0.19
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4039363 p.Ala448Pro missense_variant 0.17
clpC1 4039680 p.Phe342Ser missense_variant 0.22
clpC1 4039932 p.Gly258Val missense_variant 0.32
embC 4240646 p.Phe262Val missense_variant 0.16
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241056 c.1194C>G synonymous_variant 0.19
embC 4241456 p.Ala532Pro missense_variant 0.32
embC 4242476 p.Pro872Ala missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.17
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243977 p.Ala249Pro missense_variant 0.25
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244375 c.1143C>G synonymous_variant 0.17
embA 4244895 p.Thr555Ala missense_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 4248725 p.Ser738Ala missense_variant 0.21
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
ethA 4327672 c.-199G>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4408329 c.-127C>G upstream_gene_variant 0.24