TB-Profiler result

Run: SRR3732719
Summary

Run ID: SRR3732719

Sample name:

Date: 04-04-2023 05:38:52

Number of reads: 1149644

Percentage reads mapped: 99.59

Strain: lineage4.1

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
lineage4.1 Euro-American T;X;H None 0.99
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
gyrB 6576 p.Arg446Leu missense_variant 0.67 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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 5714 p.Lys159Glu missense_variant 0.11
gyrB 6259 c.1020C>T synonymous_variant 1.0
gyrB 6268 c.1029C>T synonymous_variant 0.2
gyrB 6507 p.Ala423Val missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Glu missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9388 p.Ala696Val missense_variant 0.14
gyrA 9656 c.2355C>G synonymous_variant 1.0
mshA 576763 p.Trp472Cys missense_variant 0.17
rpoB 760418 c.612G>T synonymous_variant 0.22
rpoB 760980 c.1174C>A synonymous_variant 0.22
rpoB 761177 c.1371G>T synonymous_variant 0.12
rpoB 761768 c.1962G>T synonymous_variant 0.2
rpoB 761788 p.Arg661Gln missense_variant 0.25
rpoB 762080 c.2274G>A synonymous_variant 0.2
rpoB 762365 c.2559C>T synonymous_variant 1.0
rpoB 762373 p.Pro856Leu missense_variant 0.18
rpoC 763383 p.Asn5Ser missense_variant 0.67
rpoC 763905 p.Ala179Asp missense_variant 0.15
rpoC 763999 p.Asp210Glu missense_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765187 c.1818C>T synonymous_variant 1.0
rpoC 766012 c.2643C>G synonymous_variant 1.0
rpoC 766054 c.2685C>A synonymous_variant 0.2
rpoC 766067 p.Glu900* stop_gained 0.22
rpoC 766738 c.3369G>T synonymous_variant 0.2
rpoC 766745 p.Gly1126Cys missense_variant 0.18
rpoC 767071 c.3702C>A synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775973 p.Leu836Phe missense_variant 1.0
mmpL5 776411 c.2070T>C synonymous_variant 1.0
mmpL5 777521 c.960C>A synonymous_variant 0.15
mmpL5 777579 p.Thr301Asn missense_variant 0.12
mmpL5 777943 p.Pro180Thr missense_variant 0.15
mmpL5 777983 c.498G>C synonymous_variant 0.12
mmpL5 778051 p.Gly144Cys missense_variant 0.13
mmpS5 778668 p.Arg80Trp missense_variant 0.29
mmpL5 778935 c.-455G>T upstream_gene_variant 0.12
mmpR5 779323 p.Ala112Ser missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 1.0
rpsL 781718 c.159C>A synonymous_variant 0.13
rpsL 781724 c.165G>T synonymous_variant 0.12
fbiC 1302961 p.Ala11Ser missense_variant 0.12
fbiC 1303584 c.654C>A synonymous_variant 0.14
fbiC 1303828 p.His300Asn missense_variant 0.12
embR 1416519 c.827_828dupTG frameshift_variant 0.18
embR 1417321 p.Lys9Asn missense_variant 0.22
atpE 1460849 c.-196G>A upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473607 n.-51C>T upstream_gene_variant 0.5
inhA 1674255 p.Asp18Glu missense_variant 0.2
rpsA 1833880 p.Trp113Cys missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918286 p.Gly116Val missense_variant 0.14
tlyA 1918542 c.603G>T synonymous_variant 0.12
katG 2154746 p.Ala456Ser missense_variant 0.17
katG 2155198 p.Gly305Val missense_variant 0.25
katG 2155407 c.705G>A synonymous_variant 0.4
katG 2156007 c.105C>T synonymous_variant 1.0
katG 2156560 c.-449C>T upstream_gene_variant 0.22
PPE35 2170308 p.Leu102Ala missense_variant 0.17
PPE35 2170313 c.300G>C synonymous_variant 0.17
Rv1979c 2221784 p.Ala461Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290067 c.-826C>T upstream_gene_variant 0.29
eis 2714355 c.978C>T synonymous_variant 0.12
folC 2746227 p.Gly458Arg missense_variant 0.18
folC 2746747 c.852G>T synonymous_variant 0.18
pepQ 2859329 c.1090C>A synonymous_variant 0.12
pepQ 2860594 c.-176C>A upstream_gene_variant 0.18
ribD 2987100 p.Val88Leu missense_variant 0.17
Rv2752c 3065478 p.Phe238Leu missense_variant 0.2
thyX 3067300 p.Leu216Met missense_variant 0.14
thyX 3067774 p.Ala58Thr missense_variant 0.2
thyX 3067934 c.12C>A synonymous_variant 0.2
thyA 3073802 p.Pro224Thr missense_variant 0.12
thyA 3073898 p.Ala192Ser missense_variant 0.14
thyA 3074245 p.Gly76Val missense_variant 0.17
thyA 3074325 c.147A>G synonymous_variant 0.25
thyA 3074415 c.57C>T synonymous_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086889 p.Ala24Ser missense_variant 0.29
ald 3087256 p.Ala146Asp missense_variant 0.11
ald 3087422 c.603C>A synonymous_variant 0.22
fbiD 3339460 p.Gly115Cys missense_variant 0.12
Rv3083 3449178 p.Lys225Asn missense_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474541 p.Ala179Pro missense_variant 0.14
fprA 3474623 p.Ala206Val missense_variant 0.15
fprA 3474717 c.711C>T synonymous_variant 0.13
whiB7 3568827 c.-148G>C upstream_gene_variant 0.15
fbiB 3640617 c.-918G>T upstream_gene_variant 0.17
fbiA 3641159 p.Ala206Asp missense_variant 0.13
fbiB 3642627 p.Arg365Cys missense_variant 0.15
alr 3841413 p.Arg3Leu missense_variant 0.25
alr 3841425 c.-5G>T upstream_gene_variant 0.25
rpoA 3878132 p.Ala126Ser missense_variant 0.12
ddn 3987062 c.219C>A synonymous_variant 0.22
clpC1 4040042 c.663C>A synonymous_variant 0.2
embC 4240136 p.Ala92Thr missense_variant 0.15
embC 4240588 c.726C>T synonymous_variant 0.22
embC 4241504 p.Val548Met missense_variant 1.0
embC 4241587 c.1725C>A synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242957 p.Pro1032Gln missense_variant 0.17
embA 4244006 c.774C>T synonymous_variant 0.2
embA 4244304 c.1072C>A synonymous_variant 0.15
embA 4244539 p.Ala436Val missense_variant 0.33
embA 4244704 p.Pro491Gln missense_variant 0.2
embA 4245103 p.Trp624Leu missense_variant 0.22
embB 4246488 c.-26C>A upstream_gene_variant 0.12
embB 4246817 p.Ala102Thr missense_variant 0.14
embB 4248375 p.Trp621* stop_gained 0.2
embB 4248718 p.Asn735Lys missense_variant 0.15
embB 4248909 p.Ala799Asp missense_variant 0.17
embB 4249766 p.Arg1085Ser missense_variant 0.4
aftB 4267391 c.1446G>T synonymous_variant 0.22
ubiA 4269162 p.Leu224Phe missense_variant 0.25
ethA 4327300 p.Asp58Glu missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
PPE35 2170007 c.544_605delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG frameshift_variant 1.0