TB-Profiler result

Run: SRR13837498
Summary

Run ID: SRR13837498

Sample name:

Date: 03-04-2023 09:11:54

Number of reads: 594336

Percentage reads mapped: 97.1

Strain: lineage4.9

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
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
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 5149 c.-91G>C upstream_gene_variant 1.0
gyrB 7090 p.Asp617Glu missense_variant 1.0
gyrA 8436 p.Tyr379Asn missense_variant 0.9
fgd1 491701 p.His307Asn missense_variant 1.0
ccsA 619765 c.-126G>A upstream_gene_variant 1.0
ccsA 620283 c.393T>C synonymous_variant 0.11
ccsA 620284 p.Ala132Pro missense_variant 0.11
ccsA 620288 p.Arg133Gln missense_variant 0.11
ccsA 620340 c.450C>G synonymous_variant 0.14
ccsA 620362 p.Ala158Thr missense_variant 0.15
ccsA 620367 c.477T>C synonymous_variant 0.15
ccsA 620373 c.483C>G synonymous_variant 0.14
ccsA 620376 c.486G>C synonymous_variant 0.15
ccsA 620385 c.495G>C synonymous_variant 0.16
ccsA 620388 c.498A>G synonymous_variant 0.15
ccsA 620389 c.499C>T synonymous_variant 0.15
ccsA 620412 c.522T>C synonymous_variant 0.12
ccsA 620415 c.525T>C synonymous_variant 0.12
rpoC 763411 c.42T>G synonymous_variant 0.11
rpoC 763414 c.45T>C synonymous_variant 0.11
rpoC 763486 c.117T>G synonymous_variant 0.16
rpoC 763492 c.123G>C synonymous_variant 0.12
rpoC 763570 c.201G>C synonymous_variant 0.12
rpoC 763573 c.204G>C synonymous_variant 0.12
rpoC 763594 c.225C>T synonymous_variant 0.13
rpoC 763603 c.234C>T synonymous_variant 0.14
mmpL5 775867 p.Arg872Gly missense_variant 1.0
mmpL5 776710 p.Cys591Ser missense_variant 1.0
mmpL5 777625 p.Gln286Lys missense_variant 1.0
mmpS5 778811 p.Phe32Ser missense_variant 1.0
fbiC 1303914 c.984C>G synonymous_variant 0.12
embR 1416901 c.447G>C synonymous_variant 0.96
rrl 1474466 n.810delA non_coding_transcript_exon_variant 1.0
rrl 1475224 n.1567T>C non_coding_transcript_exon_variant 1.0
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.12
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12
rrl 1476589 n.2932G>A non_coding_transcript_exon_variant 1.0
rpsA 1834375 c.834G>A synonymous_variant 0.13
rpsA 1834378 c.837T>C synonymous_variant 0.12
rpsA 1834396 c.855G>C synonymous_variant 0.14
rpsA 1834411 c.870T>C synonymous_variant 0.13
PPE35 2170487 c.126T>A synonymous_variant 1.0
Rv1979c 2221853 p.Phe438Ile missense_variant 1.0
ribD 2987369 c.531G>A synonymous_variant 1.0
thyA 3073975 p.Arg166Pro missense_variant 0.96
Rv3236c 3612013 c.1104A>T synonymous_variant 1.0
Rv3236c 3612032 p.Met362Arg missense_variant 1.0
rpoA 3877692 c.816G>C synonymous_variant 0.12
rpoA 3877704 c.804G>C synonymous_variant 0.11
rpoA 3877743 c.765T>C synonymous_variant 0.17
rpoA 3877764 c.744C>G synonymous_variant 0.18
rpoA 3877770 c.738A>G synonymous_variant 0.18
rpoA 3877776 c.732T>C synonymous_variant 0.21
rpoA 3877782 c.726T>C synonymous_variant 0.21
rpoA 3877791 c.717C>G synonymous_variant 0.15
rpoA 3877818 c.690A>G synonymous_variant 0.17
rpoA 3878001 c.507A>G synonymous_variant 0.17
rpoA 3878022 c.486T>C synonymous_variant 0.2
rpoA 3878028 c.480G>C synonymous_variant 0.15
rpoA 3878031 c.477T>C synonymous_variant 0.23
rpoA 3878040 c.468T>C synonymous_variant 0.14
rpoA 3878043 c.465G>A synonymous_variant 0.14
clpC1 4038486 p.Gly740Asp missense_variant 0.12
clpC1 4038596 c.2109A>G synonymous_variant 0.12
clpC1 4038623 c.2082A>G synonymous_variant 0.15
clpC1 4038640 p.Asp689Asn missense_variant 0.14
clpC1 4038653 c.2052C>T synonymous_variant 0.15
clpC1 4038658 p.Lys683Gln missense_variant 0.14
clpC1 4038661 p.Ser682Thr missense_variant 0.14
clpC1 4038662 c.2043T>C synonymous_variant 0.14
embC 4240425 p.Arg188Pro missense_variant 1.0
embC 4240477 c.615C>A synonymous_variant 1.0
embA 4244214 p.Ala328Ser missense_variant 1.0
embA 4244849 c.1617C>G synonymous_variant 1.0
embB 4247198 p.Thr229Pro missense_variant 1.0
embB 4247381 p.Trp290Arg missense_variant 0.96
aftB 4268115 p.Leu241Arg missense_variant 1.0
aftB 4268696 c.141G>A synonymous_variant 1.0
ethA 4326298 c.1176G>A synonymous_variant 1.0
whiB6 4338567 c.-46C>A upstream_gene_variant 1.0