TB-Profiler result

Run: SRR1657101
Summary

Run ID: SRR1657101

Sample name:

Date: 03-04-2023 17:44:04

Number of reads: 110958

Percentage reads mapped: 99.31

Strain: lineage4.9;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 0.15
La1.8 M.bovis None None 0.12
La1.8.1 M.bovis None None 1.0
lineage4.9 Euro-American (H37Rv-like) T1 None 0.93
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 5378 p.Trp47Arg missense_variant 0.4
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 8285 c.984C>T synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576105 p.Arg253Leu missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.38
rpoB 762260 c.2454C>A synonymous_variant 0.33
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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.4
rrl 1474838 n.1181C>A non_coding_transcript_exon_variant 0.25
fabG1 1673380 c.-60C>G upstream_gene_variant 0.5
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_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
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
PPE35 2169660 p.Asn318Ser missense_variant 0.33
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
eis 2715125 p.Thr70Ala missense_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.43
ribD 2987075 p.Asp79Glu missense_variant 1.0
Rv2752c 3064898 p.Val432Ile missense_variant 0.67
ald 3086709 c.-111G>T upstream_gene_variant 0.13
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 3475174 p.Lys390Glu missense_variant 1.0
fbiB 3641590 p.Gly19Glu missense_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4039151 c.1554C>T synonymous_variant 0.2
clpC1 4040240 c.465C>A synonymous_variant 0.33
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala 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