TB-Profiler result

Run: SRR3675589

Summary

Run ID: SRR3675589

Sample name:

Date: 04-04-2023 05:35:23

Number of reads: 891997

Percentage reads mapped: 83.39

Strain: lineage4

Drug-resistance: Sensitive


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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
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
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 5954 p.Glu239Lys missense_variant 0.13
gyrB 6061 p.Ser274Arg missense_variant 1.0
gyrB 6402 p.Cys388Ser missense_variant 0.1
gyrB 6790 p.Phe517Leu missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759628 c.-179C>T upstream_gene_variant 1.0
rpoB 759995 c.189C>A synonymous_variant 0.11
rpoB 760550 p.Phe248Leu missense_variant 0.11
rpoB 761450 c.1644C>T synonymous_variant 0.11
rpoC 763639 c.270G>A synonymous_variant 0.18
rpoC 764109 p.Arg247His missense_variant 0.12
rpoC 766726 c.3357T>C synonymous_variant 0.14
rpoC 766738 c.3369G>T synonymous_variant 0.12
rpoC 766749 c.3381C>G synonymous_variant 0.12
rpoC 766765 c.3396A>C synonymous_variant 0.1
rpoC 766774 c.3405T>C synonymous_variant 0.1
rpoC 766804 c.3435A>G synonymous_variant 0.15
rpoC 766843 c.3474T>C synonymous_variant 0.15
rpoC 766861 c.3492G>C synonymous_variant 0.16
rpoC 766864 c.3495G>C synonymous_variant 0.16
rpoC 766900 c.3531T>C synonymous_variant 0.1
rpoC 766933 c.3564A>G synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776697 p.Pro595Gln missense_variant 0.13
mmpL5 776924 c.1557G>A synonymous_variant 0.12
mmpL5 776961 p.Ser507Ile missense_variant 0.12
mmpL5 778458 p.Ala8Val missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781763 c.204C>T synonymous_variant 0.14
rplC 800852 p.Gln15Arg missense_variant 0.11
rplC 801025 p.Ala73Thr missense_variant 0.15
fbiC 1303016 p.Val29Gly missense_variant 0.38
Rv1258c 1407255 p.Ala29Glu missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.5
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.5
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.5
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.5
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.5
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.5
rrs 1473226 n.1381C>A non_coding_transcript_exon_variant 0.33
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 1.0
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 1.0
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 1.0
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 1.0
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 1.0
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 1.0
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0
rrl 1476512 n.2855C>G non_coding_transcript_exon_variant 1.0
inhA 1673628 c.-574C>A upstream_gene_variant 0.15
rpsA 1833634 p.Lys31Asn missense_variant 0.18
rpsA 1833879 p.Trp113Leu missense_variant 0.33
rpsA 1834103 p.Arg188Cys missense_variant 0.12
rpsA 1834375 c.834G>C synonymous_variant 0.1
rpsA 1834406 p.Arg289Ser missense_variant 0.11
rpsA 1834411 c.870T>G synonymous_variant 0.11
rpsA 1834414 c.873C>T synonymous_variant 0.11
rpsA 1834417 c.876G>C synonymous_variant 0.17
rpsA 1834420 c.879C>T synonymous_variant 0.12
rpsA 1834423 c.882G>C synonymous_variant 0.12
rpsA 1834429 c.888C>T synonymous_variant 0.12
rpsA 1834438 c.897C>T synonymous_variant 0.14
rpsA 1834451 c.910T>C synonymous_variant 0.19
rpsA 1834456 c.915T>G synonymous_variant 0.2
rpsA 1834468 c.927A>G synonymous_variant 0.18
rpsA 1834477 c.936C>T synonymous_variant 0.12
rpsA 1834489 c.948T>C synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.23
katG 2154206 p.Ala636Thr missense_variant 0.11
katG 2156536 c.-425C>A upstream_gene_variant 0.12
PPE35 2169140 c.1473G>T synonymous_variant 0.2
PPE35 2169509 c.1104T>C synonymous_variant 0.12
PPE35 2169823 p.Ala264Thr missense_variant 0.11
Rv1979c 2222200 p.Gly322Asp missense_variant 0.13
Rv1979c 2223233 c.-69G>T upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517993 c.-122G>C upstream_gene_variant 0.14
kasA 2518236 p.Ser41Ile missense_variant 0.2
ahpC 2726537 c.345G>A synonymous_variant 1.0
pepQ 2859470 p.Leu317Met missense_variant 0.12
ribD 2987316 p.Ala160Pro missense_variant 0.11
fbiD 3339273 c.156T>G synonymous_variant 0.21
fprA 3474299 p.Asp98Gly missense_variant 1.0
fprA 3474448 p.Ala148Thr missense_variant 1.0
Rv3236c 3612859 c.258G>C synonymous_variant 0.14
Rv3236c 3612961 c.156C>T synonymous_variant 0.14
fbiA 3640417 c.-126C>T upstream_gene_variant 0.15
rpoA 3878050 p.Arg153Leu missense_variant 0.12
rpoA 3878334 c.174T>C synonymous_variant 0.11
panD 4043957 p.Asp109Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244520 c.1292delC frameshift_variant 0.11
embB 4249721 p.Leu1070Met missense_variant 0.11
aftB 4269807 c.-971T>C upstream_gene_variant 0.1
ethA 4328317 c.-844C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0