TB-Profiler result

Run: SRR4035747
Summary

Run ID: SRR4035747

Sample name:

Date: 04-04-2023 07:16:23

Number of reads: 1349111

Percentage reads mapped: 99.51

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;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 5136 c.-104A>G upstream_gene_variant 0.11
gyrB 6697 p.Ile486Met missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7464 p.Val55Met missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7604 p.Gln101His missense_variant 0.11
gyrA 7698 p.Arg133Trp missense_variant 0.22
gyrA 7705 p.Thr135Ser missense_variant 0.22
gyrA 7855 p.Met185Lys missense_variant 0.13
gyrA 7920 p.Asn207Asp missense_variant 0.14
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491117 p.Asn112Ser missense_variant 0.12
fgd1 491135 p.Tyr118Cys missense_variant 0.11
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 576576 p.Ala410Val missense_variant 0.2
ccsA 620165 p.Leu92Pro missense_variant 0.18
ccsA 620330 p.Ile147Thr missense_variant 0.11
ccsA 620665 p.Trp259Arg missense_variant 0.11
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762703 p.Val966Glu missense_variant 0.13
rpoB 762926 c.3123delG frameshift_variant 0.11
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764528 p.Arg387Ser missense_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 0.95
rpoC 766600 c.3231C>T synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775912 p.Arg857Gly missense_variant 0.13
mmpL5 775913 c.2568C>T synonymous_variant 0.14
mmpL5 775922 c.2559G>T synonymous_variant 0.17
mmpL5 775946 c.2535C>T synonymous_variant 0.13
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777329 c.1152C>A synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461108 p.Ile22Val missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471706 n.-140A>G upstream_gene_variant 0.11
rrs 1472327 n.482G>T non_coding_transcript_exon_variant 0.17
rrs 1472649 n.804T>C non_coding_transcript_exon_variant 0.12
rrs 1472879 n.1034T>A non_coding_transcript_exon_variant 0.18
rrl 1473467 n.-191A>G upstream_gene_variant 0.12
rrl 1475750 n.2096delC non_coding_transcript_exon_variant 0.22
rrl 1475879 n.2222T>A non_coding_transcript_exon_variant 0.4
inhA 1673841 c.-361A>G upstream_gene_variant 0.11
inhA 1674984 p.Asp261Glu missense_variant 0.17
rpsA 1833713 p.Lys58Glu missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102829 p.Thr72Ala missense_variant 0.1
katG 2156226 c.-115T>A upstream_gene_variant 0.15
PPE35 2169180 p.Pro478Leu missense_variant 0.14
PPE35 2169662 c.951T>C synonymous_variant 0.18
Rv1979c 2222533 p.Ala211Gly missense_variant 0.12
Rv1979c 2222822 p.Ser115Pro missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519314 c.1201delT frameshift_variant 0.13
Rv2752c 3064691 p.Pro501Ser missense_variant 0.2
Rv2752c 3065287 p.Leu302Ser missense_variant 0.13
Rv2752c 3065728 p.Ala155Val missense_variant 0.18
thyA 3074076 c.396C>T synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338970 c.-147delA upstream_gene_variant 0.11
Rv3083 3449497 p.Lys332Glu missense_variant 0.16
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
alr 3841496 c.-76A>T upstream_gene_variant 0.13
clpC1 4038753 p.Gln651Arg missense_variant 0.11
clpC1 4038761 c.1944C>G synonymous_variant 0.11
clpC1 4039659 p.Glu349Gly missense_variant 0.12
clpC1 4040526 p.Arg60His missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244799 p.Val523Met missense_variant 0.18
embA 4244804 p.Leu524Phe missense_variant 0.2
embA 4245066 p.Phe612Leu missense_variant 0.1
aftB 4268002 c.835C>T synonymous_variant 0.12
ethR 4327675 p.Ala43Thr missense_variant 0.13
whiB6 4338187 p.Ser112Cys missense_variant 0.1
whiB6 4338414 p.Gln36His missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0