TB-Profiler result

Run: SRR9940974
Summary

Run ID: SRR9940974

Sample name:

Date: 04-04-2023 23:02:43

Number of reads: 516372

Percentage reads mapped: 99.92

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
pncA 2288961 p.Phe94Cys missense_variant 0.4 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
gyrA 8732 c.1431G>A synonymous_variant 0.14
gyrA 9012 p.Thr571Ala missense_variant 0.11
gyrA 9514 p.Glu738Ala missense_variant 0.12
gyrA 9678 p.Lys793Glu missense_variant 0.13
mshA 576468 p.Val374Gly missense_variant 0.11
mshA 576660 p.Leu438Ser missense_variant 0.29
ccsA 620748 c.858T>G synonymous_variant 0.5
rpoB 759859 p.Pro18Gln missense_variant 0.13
rpoB 762337 p.Ile844Thr missense_variant 0.12
rpoC 764886 p.Arg506Leu missense_variant 0.22
rpoC 765212 p.Pro615Thr missense_variant 0.11
rpoC 767157 p.Gly1263Asp missense_variant 0.12
mmpL5 778108 p.Ser125Thr missense_variant 0.12
rplC 800611 c.-198T>C upstream_gene_variant 0.18
fbiC 1304159 p.Val410Gly missense_variant 0.33
fbiC 1304794 p.Lys622* stop_gained 0.25
embR 1416830 p.Ala173Val missense_variant 0.17
embR 1417224 c.124T>C synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473061 n.1216T>C non_coding_transcript_exon_variant 0.11
rrl 1474084 n.431delA non_coding_transcript_exon_variant 0.13
rrl 1475040 n.1385delA non_coding_transcript_exon_variant 0.25
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.11
rrl 1475757 n.2101_2104delACCC non_coding_transcript_exon_variant 0.11
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.1
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.1
fabG1 1673380 c.-60C>G upstream_gene_variant 0.18
rpsA 1833803 c.265dupC frameshift_variant 0.1
rpsA 1834172 c.632delT frameshift_variant 0.11
ndh 2102341 c.702C>T synonymous_variant 0.18
katG 2155175 p.Ile313Val missense_variant 0.14
katG 2156293 c.-182C>T upstream_gene_variant 0.11
PPE35 2168855 c.1758T>C synonymous_variant 0.12
PPE35 2169848 p.Asn255Lys missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.3
PPE35 2170053 p.Thr187Ser missense_variant 0.22
PPE35 2170147 p.Ser156Ala missense_variant 0.13
PPE35 2170350 p.Thr88Asn missense_variant 0.12
PPE35 2170521 p.Trp31Leu missense_variant 0.12
PPE35 2170598 c.15G>A synonymous_variant 1.0
Rv1979c 2222000 p.Val389Met missense_variant 0.2
Rv1979c 2222117 p.Met350Val missense_variant 0.15
Rv1979c 2222541 c.624T>C synonymous_variant 0.2
kasA 2518600 c.486C>A synonymous_variant 0.2
ahpC 2726338 p.Val49Gly missense_variant 0.38
ahpC 2726341 p.Val50Gly missense_variant 0.29
thyA 3074567 c.-96C>A upstream_gene_variant 0.14
ald 3087101 p.Phe94Leu missense_variant 0.15
Rv3083 3449079 p.Leu192Phe missense_variant 0.33
Rv3083 3449520 c.1017C>A synonymous_variant 0.17
Rv3236c 3612832 c.285C>T synonymous_variant 0.14
alr 3841418 c.2dupT frameshift_variant 0.14
rpoA 3877752 p.Asp252Glu missense_variant 0.13
clpC1 4038986 c.1719C>T synonymous_variant 0.13
embC 4241589 p.Phe576Ser missense_variant 0.14
embC 4242736 c.2875dupG frameshift_variant 0.15
embA 4246200 p.Gln990Lys missense_variant 0.11
aftB 4267250 c.1587C>T synonymous_variant 0.15
aftB 4267906 p.Val311Met missense_variant 0.29
aftB 4267922 c.915G>A synonymous_variant 0.25
aftB 4269816 c.-980G>T upstream_gene_variant 0.15
gid 4408417 c.-215G>T upstream_gene_variant 0.12