TB-Profiler result

Run: SRR4037686
Summary

Run ID: SRR4037686

Sample name:

Date: 04-04-2023 07:35:46

Number of reads: 560562

Percentage reads mapped: 99.52

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
ethA 4327294 p.Tyr60* stop_gained 0.13 ethionamide
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 6248 p.Leu337Ile missense_variant 0.12
gyrB 6886 p.Phe549Leu missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7499 c.198G>T synonymous_variant 0.25
gyrA 7529 c.228G>T synonymous_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7594 p.Arg98His missense_variant 0.22
gyrA 8826 p.Asp509Tyr missense_variant 0.4
gyrA 8843 p.Glu514Asp missense_variant 0.5
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9798 p.Ala833Ser missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575378 p.Gly11Trp missense_variant 0.2
mshA 575643 p.Pro99Gln missense_variant 0.2
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620211 p.Trp107Cys missense_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761164 p.Gly453Val missense_variant 0.14
rpoB 762080 c.2274G>T synonymous_variant 0.18
rpoC 762488 c.-882G>T upstream_gene_variant 0.18
rpoB 762903 p.Asp1033Tyr missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763088 c.-282C>A upstream_gene_variant 0.17
rpoC 764209 c.840C>A synonymous_variant 0.13
rpoC 764906 p.Glu513* stop_gained 0.18
rpoC 764993 p.Ala542Ser missense_variant 0.2
rpoC 765000 p.His544Leu missense_variant 0.2
rpoC 765679 c.2310C>A synonymous_variant 0.15
rpoC 766659 p.Arg1097Leu missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775841 c.2640G>T synonymous_variant 0.22
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776900 p.Asn527Lys missense_variant 0.15
mmpL5 777461 c.1020G>A synonymous_variant 0.33
mmpL5 777499 c.982C>A synonymous_variant 0.25
mmpL5 777915 p.Ser189* stop_gained 0.17
mmpS5 779535 c.-630C>A upstream_gene_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781597 p.Arg13Leu missense_variant 0.5
rpsL 781638 p.Ser27Gly missense_variant 0.4
rpsL 781679 c.120C>A synonymous_variant 0.33
rplC 800813 p.Ala2Val missense_variant 0.17
rplC 801303 c.495G>T synonymous_variant 0.25
fbiC 1302967 p.Pro13Ser missense_variant 0.15
fbiC 1305397 p.Glu823* stop_gained 0.25
Rv1258c 1406461 p.Ala294Ser missense_variant 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416962 p.Gly129Asp missense_variant 0.17
embR 1417326 p.Glu8* stop_gained 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473609 n.-49G>T upstream_gene_variant 0.12
rrl 1474238 n.581G>T non_coding_transcript_exon_variant 0.13
rrl 1474503 n.846G>T non_coding_transcript_exon_variant 0.22
rrl 1474911 n.1254G>A non_coding_transcript_exon_variant 0.14
rrl 1475031 n.1374G>T non_coding_transcript_exon_variant 0.15
rrl 1475595 n.1938G>T non_coding_transcript_exon_variant 0.17
rrl 1476009 n.2352G>T non_coding_transcript_exon_variant 0.25
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.18
fabG1 1673944 p.Arg169Ser missense_variant 0.17
rpsA 1834110 p.Trp190* stop_gained 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834444 c.903C>A synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918337 p.Arg133Leu missense_variant 0.15
tlyA 1918611 c.672C>A synonymous_variant 0.29
ndh 2102118 p.Leu309Met missense_variant 0.22
ndh 2102216 p.Trp276Leu missense_variant 0.13
ndh 2102833 c.210G>A synonymous_variant 0.25
katG 2154317 p.Gly599Arg missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156335 c.-224C>A upstream_gene_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168476 p.Pro713Thr missense_variant 0.2
PPE35 2168947 p.Pro556Thr missense_variant 0.15
PPE35 2170101 p.Pro171Gln missense_variant 0.25
PPE35 2170103 c.510C>A synonymous_variant 0.22
Rv1979c 2222055 p.Asp370Glu missense_variant 0.13
Rv1979c 2222074 p.Pro364Gln missense_variant 0.14
Rv1979c 2222136 p.Lys343Asn missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289801 c.-560C>T upstream_gene_variant 0.4
kasA 2519207 p.Gly365Cys missense_variant 0.18
eis 2714421 c.912A>G synonymous_variant 0.22
eis 2714621 p.Val238Phe missense_variant 0.25
eis 2714673 c.660C>A synonymous_variant 0.4
eis 2714969 p.Glu122* stop_gained 0.33
ahpC 2726606 c.414C>T synonymous_variant 0.4
folC 2746260 p.Val447Phe missense_variant 0.29
ribD 2986989 p.Gly51Cys missense_variant 0.18
ribD 2987183 c.345G>T synonymous_variant 0.17
ribD 2987254 p.Ala139Glu missense_variant 0.22
Rv2752c 3064565 p.Glu543* stop_gained 0.22
Rv2752c 3064808 p.Leu462Met missense_variant 0.12
Rv2752c 3065441 p.Ala251Ser missense_variant 0.22
thyA 3073806 c.666C>G synonymous_variant 0.4
thyA 3073985 p.Leu163Ile missense_variant 0.25
thyA 3074625 c.-154G>T upstream_gene_variant 0.17
ald 3086653 c.-167C>A upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087300 p.Gly161Cys missense_variant 0.22
fbiD 3339278 p.Gly54Val missense_variant 1.0
fbiD 3339384 c.267C>A synonymous_variant 0.18
Rv3083 3448500 c.-4A>G upstream_gene_variant 0.22
Rv3083 3448586 p.Pro28His missense_variant 0.14
Rv3083 3448748 p.Arg82Leu missense_variant 0.17
Rv3083 3449883 p.Trp460Cys missense_variant 0.17
Rv3083 3449884 p.Arg461Gly missense_variant 0.17
fprA 3473923 c.-84G>T upstream_gene_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568499 p.Glu61* stop_gained 0.5
whiB7 3568532 c.148C>A synonymous_variant 0.4
whiB7 3568626 c.53delT frameshift_variant 1.0
Rv3236c 3612131 p.Ala329Glu missense_variant 0.15
Rv3236c 3612153 p.Gly322Trp missense_variant 0.15
Rv3236c 3612630 p.Ala163Ser missense_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612973 c.144C>A synonymous_variant 0.25
fbiB 3641709 c.175C>A synonymous_variant 0.25
fbiB 3642698 c.1164G>T synonymous_variant 0.29
fbiB 3642708 p.Gly392Trp missense_variant 0.29
alr 3840636 p.Pro262Gln missense_variant 0.2
alr 3841243 p.Gln60Lys missense_variant 0.29
alr 3841586 c.-166G>T upstream_gene_variant 0.15
rpoA 3877572 c.936G>A synonymous_variant 0.33
clpC1 4038175 p.Glu844* stop_gained 0.25
embC 4240720 p.Phe286Leu missense_variant 0.17
embC 4241228 p.Leu456Ile missense_variant 0.17
embC 4241236 c.1374C>A synonymous_variant 0.17
embC 4241709 p.Arg616Leu missense_variant 0.18
embC 4241952 p.Arg697Met missense_variant 0.13
embC 4242058 c.2196G>T synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242739 c.-494C>A upstream_gene_variant 0.18
embC 4242822 p.Val987Gly missense_variant 0.4
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243728 p.Lys166Glu missense_variant 0.22
embB 4248066 p.Trp518Leu missense_variant 0.22
embB 4248268 c.1755G>C synonymous_variant 0.29
aftB 4267046 p.Phe597Leu missense_variant 0.2
aftB 4267073 c.1764C>A synonymous_variant 0.17
aftB 4267088 c.1749C>A synonymous_variant 0.15
aftB 4267096 p.Pro581Thr missense_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268177 c.660G>A synonymous_variant 0.15
ubiA 4269117 p.Glu239Asp missense_variant 0.4
ethA 4326305 p.Ser390Tyr missense_variant 0.14
ethA 4326774 p.Ala234Ser missense_variant 0.15
ethA 4327950 c.-477G>T upstream_gene_variant 0.2
ethA 4328435 c.-962C>A upstream_gene_variant 0.29
whiB6 4338260 p.Arg88Trp missense_variant 1.0
whiB6 4338312 c.210G>T synonymous_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407835 p.Trp123Leu missense_variant 0.18
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408016 p.Asp63Tyr missense_variant 0.13