TB-Profiler result

Run: SRR4034419

Summary

Run ID: SRR4034419

Sample name:

Date: 04-04-2023 06:47:29

Number of reads: 848236

Percentage reads mapped: 99.73

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.1 Euro-American (S-type) S;T None 0.99
lineage4.4.1.1 Euro-American S;Orphans 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 6250 c.1011A>G synonymous_variant 1.0
gyrB 6263 p.Asp342Tyr missense_variant 0.14
gyrB 6627 p.Ala463Val missense_variant 0.22
gyrA 7334 c.33G>A synonymous_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9621 p.Leu774Met missense_variant 0.12
mshA 575516 p.Leu57Met missense_variant 0.12
mshA 576206 p.Ala287Ser missense_variant 0.12
ccsA 620106 p.Phe72Leu missense_variant 0.13
ccsA 620155 p.Gly89Trp missense_variant 0.14
ccsA 620835 c.945C>T synonymous_variant 0.17
rpoB 760079 p.Glu91Asp missense_variant 0.33
rpoB 762155 c.2349C>A synonymous_variant 0.18
rpoC 764692 c.1323C>T synonymous_variant 0.4
rpoC 766792 c.3423C>A synonymous_variant 0.15
mmpL5 775609 p.Ala958Thr missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776275 p.Ala736Ser missense_variant 0.25
mmpL5 777746 c.735G>T synonymous_variant 0.33
mmpL5 778091 p.Trp130Cys missense_variant 0.14
mmpL5 779209 c.-729G>A upstream_gene_variant 0.25
mmpR5 779384 p.Arg132Leu missense_variant 0.29
mmpR5 779455 p.Arg156* stop_gained 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781491 c.-69C>A upstream_gene_variant 0.22
rplC 801194 p.Arg129Gln missense_variant 0.29
rplC 801229 p.Ala141Thr missense_variant 0.15
rplC 801438 c.630T>C synonymous_variant 0.15
fbiC 1302987 c.57C>A synonymous_variant 0.13
fbiC 1304710 p.Ala594Thr missense_variant 0.25
fbiC 1304748 p.Asp606Glu missense_variant 0.22
fbiC 1305486 c.2556C>A synonymous_variant 0.17
Rv1258c 1407055 p.Tyr96His missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472407 n.562T>C non_coding_transcript_exon_variant 0.22
rrl 1473513 n.-145T>C upstream_gene_variant 0.18
inhA 1674240 c.39C>T synonymous_variant 0.12
rpsA 1834403 p.Ala288Ser missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102711 p.Pro111His missense_variant 0.14
ndh 2102718 p.Gln109Lys missense_variant 0.17
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2155552 p.Arg187Leu missense_variant 0.2
katG 2156013 c.99C>T synonymous_variant 0.33
PPE35 2168440 p.Ser725Pro missense_variant 0.25
PPE35 2169413 c.1200T>C synonymous_variant 0.13
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2221883 p.Leu428Met missense_variant 0.15
Rv1979c 2221977 p.Leu396Phe missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288949 p.Ala98Asp missense_variant 0.22
pncA 2289361 c.-120G>T upstream_gene_variant 0.14
kasA 2519033 p.His307Asn missense_variant 0.13
eis 2714851 p.Ser161Asn missense_variant 0.15
ahpC 2726285 c.93C>A synonymous_variant 0.25
folC 2746629 p.Asp324Asn missense_variant 0.2
pepQ 2859441 c.978C>A synonymous_variant 0.22
pepQ 2859700 p.Gly240Asp missense_variant 0.12
Rv2752c 3067063 c.-872C>T upstream_gene_variant 0.14
thyA 3074006 p.Asp156Asn missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087189 p.Asp124Tyr missense_variant 0.33
ald 3087683 c.864C>T synonymous_variant 0.14
fbiD 3339150 c.35delT frameshift_variant 0.17
fbiD 3339634 p.Ser173Thr missense_variant 0.15
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3449973 c.1470A>G synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474701 p.Gly232Val missense_variant 0.17
fprA 3475270 p.His422Asn missense_variant 0.25
whiB7 3568682 c.-3G>T upstream_gene_variant 0.18
whiB7 3568820 c.-141G>T upstream_gene_variant 0.11
Rv3236c 3612599 p.Ala173Gly missense_variant 0.15
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
alr 3840867 p.Glu185Val missense_variant 0.25
alr 3841371 p.Gly17Val missense_variant 0.33
alr 3841473 c.-53G>A upstream_gene_variant 0.22
rpoA 3877656 c.852T>C synonymous_variant 0.29
rpoA 3878396 c.112C>T synonymous_variant 0.17
rpoA 3878435 c.72delA frameshift_variant 0.17
rpoA 3878472 c.36C>T synonymous_variant 0.18
clpC1 4038757 p.Gly650Trp missense_variant 0.14
clpC1 4039147 p.Gly520Trp missense_variant 0.18
clpC1 4039223 p.Ile494Met missense_variant 0.25
embC 4240622 p.Ala254Thr missense_variant 0.13
embC 4241768 p.Ser636Gly missense_variant 0.14
embC 4242347 p.Ala829Thr missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243457 c.225C>A synonymous_variant 0.15
embA 4244069 c.837C>A synonymous_variant 0.15
embA 4244138 c.906G>A synonymous_variant 0.17
embA 4244463 p.Ala411Ser missense_variant 0.14
embA 4244488 p.Ala419Glu missense_variant 0.15
embA 4245302 c.2070G>A synonymous_variant 0.2
embA 4246483 p.Trp1084Leu missense_variant 0.12
embB 4246792 c.279C>A synonymous_variant 0.22
embB 4247818 c.1305C>T synonymous_variant 0.13
ubiA 4269761 p.Gln25Lys missense_variant 0.12
ethR 4328047 p.Pro167Thr missense_variant 0.13
whiB6 4338346 p.Arg59Leu missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407709 c.492_493dupCG frameshift_variant 0.18