TB-Profiler result

Run: SRR9940983
Summary

Run ID: SRR9940983

Sample name:

Date: 04-04-2023 23:02:12

Number of reads: 434078

Percentage reads mapped: 99.98

Strain: lineage4.9

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.9 Euro-American (H37Rv-like) T1 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
ethA 4326251 c.1222delT frameshift_variant 0.45 ethionamide
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
gyrA 8376 p.Asp359Tyr missense_variant 0.13
mshA 575401 c.54G>T synonymous_variant 0.13
ccsA 620236 p.Leu116Met missense_variant 0.33
ccsA 620411 p.Ile174Thr missense_variant 0.25
rpoB 759615 c.-192A>C upstream_gene_variant 0.29
rpoB 760633 p.Arg276Leu missense_variant 0.33
rpoB 760990 p.Arg395Leu missense_variant 0.22
rpoB 761383 p.Thr526Ile missense_variant 0.11
rpoB 762376 p.Ala857Asp missense_variant 0.22
rpoC 766254 p.Val962Glu missense_variant 0.22
mmpL5 778440 p.Pro14Arg missense_variant 0.15
mmpS5 779636 c.-731C>A upstream_gene_variant 0.25
rpsL 781686 p.Lys43* stop_gained 0.22
rpsL 781814 c.255C>A synonymous_variant 0.18
rpsL 781904 c.345C>T synonymous_variant 0.14
rplC 800722 c.-87C>A upstream_gene_variant 0.12
rplC 801022 p.Ala72Thr missense_variant 0.18
embR 1416989 c.358delA frameshift_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473969 n.312G>T non_coding_transcript_exon_variant 0.2
rrl 1474057 n.400G>T non_coding_transcript_exon_variant 0.14
rrl 1475987 n.2330G>A non_coding_transcript_exon_variant 0.4
rrl 1476360 n.2703C>A non_coding_transcript_exon_variant 0.22
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.22
fabG1 1673548 p.Ala37Ser missense_variant 0.29
tlyA 1917850 c.-90C>G upstream_gene_variant 0.33
tlyA 1918614 c.675C>A synonymous_variant 0.18
ndh 2102538 p.Lys169Gln missense_variant 0.33
katG 2154386 p.Gln576* stop_gained 0.15
katG 2155878 c.234G>A synonymous_variant 0.2
PPE35 2168507 c.2106C>T synonymous_variant 0.12
PPE35 2169442 p.Ala391Thr missense_variant 0.18
PPE35 2170598 c.15G>A synonymous_variant 1.0
Rv1979c 2223034 p.Gly44Val missense_variant 0.12
pncA 2289262 c.-21G>T upstream_gene_variant 0.18
pncA 2289799 c.-558G>T upstream_gene_variant 0.12
eis 2714698 p.Arg212His missense_variant 0.22
ribD 2987142 p.Gln102* stop_gained 0.15
ribD 2987157 p.Gln107Lys missense_variant 0.15
ribD 2987204 c.366G>A synonymous_variant 0.12
Rv2752c 3064635 c.1557G>A synonymous_variant 0.2
Rv2752c 3065972 c.217_219delGAC conservative_inframe_deletion 0.2
ald 3087246 p.Gln143Lys missense_variant 0.29
ald 3087813 p.Ala332Ser missense_variant 0.17
Rv3083 3448454 c.-50C>A upstream_gene_variant 0.17
fprA 3474664 p.Gly220Trp missense_variant 0.25
fprA 3475096 p.Pro364Ser missense_variant 0.14
Rv3236c 3612156 p.Arg321Cys missense_variant 0.18
fbiB 3641523 c.-12G>T upstream_gene_variant 0.17
alr 3840753 p.Arg223His missense_variant 0.25
rpoA 3877791 c.717C>A synonymous_variant 0.14
ddn 3986694 c.-150G>T upstream_gene_variant 0.25
clpC1 4039347 p.Arg453Gln missense_variant 0.13
clpC1 4039546 p.Asp387Asn missense_variant 0.15
clpC1 4040192 c.513C>A synonymous_variant 0.4
clpC1 4040324 c.381G>A synonymous_variant 0.25
clpC1 4040874 c.-171delT upstream_gene_variant 0.2
embC 4242048 p.Ser729Cys missense_variant 0.29
embA 4243611 c.382delC frameshift_variant 0.22
embA 4244289 p.Gly353Trp missense_variant 0.33
embA 4244726 p.Asp498Glu missense_variant 0.29
embB 4247197 c.685delA frameshift_variant 0.18
embB 4248958 p.Trp815Cys missense_variant 0.22
ubiA 4269592 p.Asp81Gly missense_variant 0.12
gid 4407642 p.Arg187Ser missense_variant 0.18
gid 4407851 p.Arg118Ser missense_variant 0.12