TB-Profiler result

Run: SRR1002701
Summary

Run ID: SRR1002701

Sample name:

Date: 02-04-2023 14:20:02

Number of reads: 407872

Percentage reads mapped: 97.19

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 5806 c.567C>A synonymous_variant 0.13
gyrB 6148 c.909C>A synonymous_variant 0.12
gyrA 7281 c.-21T>C upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8476 p.Arg392Leu missense_variant 0.15
gyrA 8504 c.1203G>T synonymous_variant 0.18
gyrA 9102 p.Ala601Thr missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490737 c.-46C>T upstream_gene_variant 0.17
fgd1 490879 p.Asp33Asn missense_variant 0.14
fgd1 491613 c.831C>T synonymous_variant 0.15
mshA 575431 c.84C>T synonymous_variant 0.33
mshA 576659 p.Leu438Met missense_variant 0.22
ccsA 620753 p.Arg288Leu missense_variant 0.14
rpoB 761128 p.Ser441* stop_gained 0.18
rpoB 761690 c.1884G>T synonymous_variant 0.29
rpoB 761741 p.Glu645Asp missense_variant 0.29
rpoC 763127 c.-243G>T upstream_gene_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766062 p.Val898Asp missense_variant 0.25
rpoC 766445 p.Gly1026Ser missense_variant 0.25
rpoC 767189 p.Pro1274Thr missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775651 c.2830C>A synonymous_variant 0.17
mmpL5 776003 c.2478C>T synonymous_variant 0.14
mmpL5 776018 c.2463G>C synonymous_variant 0.15
mmpL5 776021 c.2460G>C synonymous_variant 0.15
mmpL5 777119 p.His454Gln missense_variant 0.24
mmpL5 777122 c.1359C>T synonymous_variant 0.24
mmpL5 777128 c.1353A>G synonymous_variant 0.25
mmpL5 777596 c.885G>A synonymous_variant 0.18
mmpL5 778151 p.Asp110Glu missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303497 c.567G>A synonymous_variant 0.18
fbiC 1304539 p.Arg537Cys missense_variant 0.25
fbiC 1304618 p.Arg563Leu missense_variant 0.17
Rv1258c 1406752 p.Gly197Ser missense_variant 0.25
embR 1417255 c.93C>T synonymous_variant 0.15
embR 1417268 p.Pro27Gln missense_variant 0.12
embR 1417304 p.Leu15Pro missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475316 n.1659G>T non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15
fabG1 1673462 p.Gly8Val missense_variant 0.17
inhA 1673547 c.-655T>A upstream_gene_variant 0.18
fabG1 1673754 p.Phe105Leu missense_variant 0.15
rpsA 1833931 c.390C>A synonymous_variant 0.12
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917902 c.-38G>T upstream_gene_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101683 p.Gly454Cys missense_variant 0.29
katG 2155767 c.345C>A synonymous_variant 0.29
katG 2156196 c.-85C>T upstream_gene_variant 1.0
katG 2156568 c.-457G>A upstream_gene_variant 0.2
PPE35 2167865 c.2748G>C synonymous_variant 0.18
PPE35 2167868 c.2745A>C synonymous_variant 0.19
PPE35 2167965 p.Ala883Gly missense_variant 0.2
PPE35 2167967 c.2646A>C synonymous_variant 0.2
PPE35 2169269 c.1344A>G synonymous_variant 0.16
PPE35 2169272 c.1341C>G synonymous_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.18
Rv1979c 2222056 p.Asp370Ala missense_variant 0.33
Rv1979c 2222683 p.Trp161Leu missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289259 c.-18C>T upstream_gene_variant 0.13
pncA 2289529 c.-288G>T upstream_gene_variant 0.17
kasA 2518864 c.750G>C synonymous_variant 0.15
kasA 2518879 c.765A>G synonymous_variant 0.14
kasA 2518882 c.768C>A synonymous_variant 0.14
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519041 c.927C>T synonymous_variant 0.4
kasA 2519241 c.1127_1128insT frameshift_variant 0.29
folC 2746214 p.Ser462* stop_gained 0.33
folC 2746340 p.Ala420Val missense_variant 1.0
pepQ 2859416 p.Gly335Cys missense_variant 0.15
Rv2752c 3064971 c.1221C>A synonymous_variant 0.22
Rv2752c 3065739 c.453G>T synonymous_variant 0.2
Rv2752c 3067028 c.-837A>G upstream_gene_variant 0.29
thyX 3067825 p.Arg41Trp missense_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087276 p.Gln153Lys missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474878 p.Arg291His missense_variant 0.17
Rv3236c 3613071 p.Ala16Ser missense_variant 0.15
fbiA 3641016 p.Asp158Glu missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038773 p.Asp644Glu missense_variant 0.12
clpC1 4038776 p.Glu643Asp missense_variant 0.13
clpC1 4038782 c.1923G>C synonymous_variant 0.15
clpC1 4038968 c.1737G>A synonymous_variant 1.0
clpC1 4039645 p.His354Asp missense_variant 0.15
clpC1 4040144 c.561G>C synonymous_variant 0.5
clpC1 4040872 c.-168C>A upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243789 p.Ser186* stop_gained 0.25
embA 4244996 c.1764C>A synonymous_variant 0.18
embA 4245356 c.2124C>G synonymous_variant 0.2
embA 4246506 p.Ala1092Ser missense_variant 0.17
embB 4247478 p.Trp322Leu missense_variant 0.25
embB 4248483 p.Asn657Ile missense_variant 0.14
aftB 4267433 c.1404C>A synonymous_variant 0.14
aftB 4268441 c.396C>T synonymous_variant 0.14
aftB 4269726 c.-890G>A upstream_gene_variant 0.22
ethR 4327375 c.-174G>T upstream_gene_variant 0.17
whiB6 4338290 p.Gly78Trp missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0