TB-Profiler result

Run: SRR1049961
Summary

Run ID: SRR1049961

Sample name:

Date: 02-04-2023 18:24:52

Number of reads: 1178943

Percentage reads mapped: 97.88

Strain: lineage4.1;La1.6

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 0.74
La1.6 M.bovis None None 0.81
lineage4 Euro-American LAM;T;S;X;H None 0.24
lineage4.1 Euro-American T;X;H None 0.18
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 0.71 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 0.65
gyrA 6406 c.-896C>T upstream_gene_variant 0.77
gyrB 6446 p.Ala403Ser missense_variant 0.8
gyrB 6507 p.Ala423Val missense_variant 0.2
gyrA 7042 c.-260C>T upstream_gene_variant 0.85
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7654 p.Ser118Leu missense_variant 0.12
gyrA 8285 c.984C>T synonymous_variant 0.87
gyrA 9143 c.1842T>C synonymous_variant 0.89
gyrA 9217 p.Asp639Ala missense_variant 0.83
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9484 p.Ser728Leu missense_variant 0.91
gyrA 9656 c.2355C>G synonymous_variant 0.3
fgd1 491111 p.Ala110Glu missense_variant 0.12
fgd1 491172 c.390C>G synonymous_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 0.86
mshA 575547 c.201_202delCA frameshift_variant 0.12
ccsA 620045 p.Gly52Val missense_variant 0.22
ccsA 620768 p.Ala293Gly missense_variant 0.76
rpoC 763031 c.-339T>C upstream_gene_variant 0.97
rpoC 764176 c.807C>T synonymous_variant 0.63
rpoC 765150 p.Gly594Glu missense_variant 0.14
rpoC 765187 c.1818C>T synonymous_variant 0.25
rpoC 766012 c.2643C>G synonymous_variant 0.54
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775973 p.Leu836Phe missense_variant 0.19
mmpL5 776100 p.Thr794Ile missense_variant 0.81
mmpL5 776411 c.2070T>C synonymous_variant 0.33
mmpL5 776750 c.1731C>T synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801319 p.Gly171Cys missense_variant 0.12
fbiC 1302899 c.-32A>G upstream_gene_variant 0.82
Rv1258c 1406732 c.608delC frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476022 n.2365A>G non_coding_transcript_exon_variant 0.8
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918184 p.Ala82Val missense_variant 0.18
ndh 2103173 c.-132delG upstream_gene_variant 0.78
katG 2154369 c.1743G>A synonymous_variant 0.7
katG 2154724 p.Arg463Leu missense_variant 0.71
katG 2155503 c.609C>T synonymous_variant 0.86
katG 2156007 c.105C>T synonymous_variant 0.18
katG 2156025 c.87C>A synonymous_variant 0.81
PPE35 2167926 p.Leu896Ser missense_variant 0.7
PPE35 2168011 p.Ser868Arg missense_variant 0.62
PPE35 2168319 p.Thr765Ile missense_variant 0.89
PPE35 2168814 c.1798dupA frameshift_variant 0.96
PPE35 2170460 c.153G>A synonymous_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 0.67
Rv1979c 2223062 p.Thr35Ala missense_variant 0.88
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289406 c.-165G>T upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 0.87
kasA 2518471 c.357C>T synonymous_variant 0.12
folC 2746245 p.Ala452Thr missense_variant 0.86
folC 2747083 c.516G>A synonymous_variant 0.12
ribD 2987615 c.777A>G stop_lost&splice_region_variant 0.78
ald 3086728 c.-92C>T upstream_gene_variant 0.83
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.88
Rv3083 3448783 p.Val94Ile missense_variant 0.77
Rv3083 3449371 p.Tyr290His missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 0.73
fprA 3475159 p.Asn385Asp missense_variant 0.7
alr 3840288 p.Asp378Gly missense_variant 0.1
rpoA 3878630 c.-124delC upstream_gene_variant 0.69
rpoA 3878652 c.-145C>T upstream_gene_variant 0.21
clpC1 4038403 c.2302T>C synonymous_variant 0.75
panD 4044479 c.-198C>T upstream_gene_variant 0.23
embC 4240671 p.Thr270Ile missense_variant 0.86
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242712 c.-521G>A upstream_gene_variant 0.14
embC 4242714 p.Asp951Gly missense_variant 0.14
embC 4242803 p.Val981Leu missense_variant 0.17
embA 4242970 c.-263C>T upstream_gene_variant 0.89
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246551 p.Asn13Ser missense_variant 0.87
embB 4246864 c.351C>T synonymous_variant 0.53
embB 4247646 p.Glu378Ala missense_variant 0.54
embB 4247791 c.1278C>T synonymous_variant 0.82
aftB 4267858 p.Ile327Val missense_variant 0.88
aftB 4269351 c.-515C>T upstream_gene_variant 0.84
ubiA 4269387 p.Glu149Asp missense_variant 0.88
aftB 4269606 c.-770T>C upstream_gene_variant 0.76
ethA 4328052 c.-579G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.74
gid 4407893 p.Met104Val missense_variant 0.84