TB-Profiler result

Run: SRR1657057
Summary

Run ID: SRR1657057

Sample name:

Date: 03-04-2023 17:43:51

Number of reads: 914742

Percentage reads mapped: 98.89

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 5179 c.-61G>A upstream_gene_variant 0.18
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 7908 p.Trp203Arg missense_variant 0.25
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
gyrA 9623 c.2322G>A synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.33
rpoB 759725 c.-82A>T upstream_gene_variant 0.14
rpoB 762320 c.2514C>T synonymous_variant 0.18
rpoB 762912 p.His1036Asn missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766997 p.Ile1210Val missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775735 p.Phe916Val missense_variant 0.33
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 1305276 c.2346G>A synonymous_variant 0.2
fbiC 1305404 p.Gly825Val missense_variant 0.2
Rv1258c 1407133 p.Gly70Arg missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.14
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.17
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.17
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.12
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.14
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.17
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.14
rrl 1474552 n.895C>G non_coding_transcript_exon_variant 0.33
rrl 1474570 n.913G>T non_coding_transcript_exon_variant 0.33
rrl 1474578 n.921A>G non_coding_transcript_exon_variant 0.5
rrl 1474584 n.927C>G non_coding_transcript_exon_variant 0.5
rrl 1474586 n.929T>A non_coding_transcript_exon_variant 0.5
rrl 1474587 n.930G>A non_coding_transcript_exon_variant 0.5
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918241 p.Leu101Gln missense_variant 0.25
ndh 2102699 p.Leu115Gln missense_variant 0.14
ndh 2102738 p.Glu102Gly missense_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2153917 p.Met732Lys missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155282 p.Gly277Asp missense_variant 0.2
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2155581 c.531C>A synonymous_variant 0.17
katG 2155894 p.Val73Ala missense_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
katG 2156417 c.-306T>G upstream_gene_variant 0.25
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 2222416 p.Arg250Gln missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714128 p.Phe402Ser missense_variant 0.25
eis 2714317 p.Arg339Gln missense_variant 0.33
eis 2715125 p.Thr70Ala missense_variant 1.0
ahpC 2726309 c.117C>T synonymous_variant 0.29
folC 2746256 p.Asp448Val missense_variant 0.25
folC 2746908 p.Val231Phe missense_variant 0.14
folC 2747654 c.-56C>T upstream_gene_variant 0.13
pepQ 2860554 c.-136G>T upstream_gene_variant 0.22
ribD 2987102 c.264G>A synonymous_variant 0.25
Rv2752c 3064876 p.Ser439Tyr missense_variant 0.12
Rv2752c 3066208 c.-17C>A upstream_gene_variant 0.5
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
ald 3087916 p.Pro366Leu missense_variant 0.2
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
Rv3236c 3612164 p.Val318Ala missense_variant 0.25
Rv3236c 3612257 p.Leu287Pro missense_variant 0.14
Rv3236c 3613247 c.-131C>T upstream_gene_variant 1.0
Rv3236c 3613300 c.-184C>A upstream_gene_variant 0.12
Rv3236c 3613303 c.-187C>A upstream_gene_variant 0.14
fbiA 3640429 c.-114C>T upstream_gene_variant 1.0
alr 3841017 p.Leu135Pro missense_variant 0.25
rpoA 3878184 c.324C>T synonymous_variant 0.2
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4038749 c.1956C>A synonymous_variant 0.12
clpC1 4040176 p.Asn177Asp missense_variant 0.11
panD 4043874 c.408C>A synonymous_variant 0.2
embC 4241250 p.Arg463His missense_variant 0.11
embC 4241432 p.Met524Val missense_variant 0.25
embC 4242563 p.Ala901Thr missense_variant 0.33
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
embA 4246417 p.Arg1062Gln missense_variant 0.14
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 4248241 c.1728C>A synonymous_variant 0.2
aftB 4267545 p.Asp431Gly missense_variant 0.2
aftB 4267784 c.1053G>A synonymous_variant 0.2
aftB 4267838 p.Phe333Leu missense_variant 0.25
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268844 c.-8A>G upstream_gene_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
ubiA 4269841 c.-8G>T upstream_gene_variant 0.17
ethA 4328196 c.-723G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408017 c.186T>C synonymous_variant 0.33