TB-Profiler result

Run: SRR11972166
Summary

Run ID: SRR11972166

Sample name:

Date: 03-04-2023 05:30:37

Number of reads: 598319

Percentage reads mapped: 98.46

Strain: lineage1.1.3.1

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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.1 Indo-Oceanic NA RD239 0.58
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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576459 c.1117_1147delGCGGTGGGCGGGCTGCCCGTCGCGGTGCGCG frameshift_variant 0.67
mshA 576544 c.1197C>A synonymous_variant 0.5
ccsA 620839 p.Leu317Met missense_variant 0.12
rpoB 760862 c.1056G>T synonymous_variant 0.17
rpoB 761152 p.Leu449Gln missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763223 c.-147C>A upstream_gene_variant 0.18
rpoC 763834 p.Met155Ile missense_variant 0.33
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764040 p.Ser224Ile missense_variant 0.2
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 766228 p.Leu953Phe missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776006 c.2475C>T synonymous_variant 0.31
mmpL5 776009 c.2472A>G synonymous_variant 0.15
mmpL5 776018 c.2463G>C synonymous_variant 0.29
mmpL5 776021 c.2460G>C synonymous_variant 0.27
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776194 p.Ala763Thr missense_variant 0.2
mmpL5 776407 p.Pro692Ser missense_variant 0.15
mmpL5 776429 c.2052C>A synonymous_variant 0.14
mmpL5 776826 p.Glu552Gly missense_variant 0.35
mmpL5 777172 p.His437Asn missense_variant 0.13
mmpL5 777739 p.Ala248Thr missense_variant 0.15
mmpL5 777911 c.570C>T synonymous_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472184 n.339T>G non_coding_transcript_exon_variant 0.15
rrs 1472193 n.348A>G non_coding_transcript_exon_variant 0.22
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.65
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.62
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.5
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.4
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.35
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.14
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.27
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.29
rrs 1472350 n.505C>T non_coding_transcript_exon_variant 0.3
rrs 1472373 n.528G>A non_coding_transcript_exon_variant 0.33
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.33
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.37
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.33
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.28
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.28
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.24
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.26
rrs 1472815 n.970A>C non_coding_transcript_exon_variant 0.56
fabG1 1673380 c.-60C>G upstream_gene_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154136 p.Val659Glu missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167814 c.2799C>T synonymous_variant 0.27
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168124 p.Gly830Glu missense_variant 0.2
PPE35 2168357 c.2256T>C synonymous_variant 0.14
PPE35 2168895 p.Gly573Val missense_variant 0.14
PPE35 2169269 c.1344A>G synonymous_variant 0.4
PPE35 2169272 c.1341C>G synonymous_variant 0.36
PPE35 2169278 c.1335T>C synonymous_variant 0.3
PPE35 2169281 c.1332T>G synonymous_variant 0.3
PPE35 2169287 c.1326T>C synonymous_variant 0.19
PPE35 2169630 p.Asn328Ser missense_variant 0.46
PPE35 2169757 p.Asn286Asp missense_variant 0.31
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.47
PPE35 2170147 p.Ser156Ala missense_variant 0.21
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289921 c.-680A>T upstream_gene_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518495 p.Asp127Glu missense_variant 0.22
kasA 2519338 c.1224T>C synonymous_variant 0.5
eis 2715305 p.Glu10* stop_gained 0.56
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.27
folC 2746872 p.Glu243* stop_gained 0.22
folC 2747420 p.Pro60His missense_variant 0.18
pepQ 2859373 p.Pro349Gln missense_variant 0.18
ribD 2986995 p.Ala53Thr missense_variant 0.18
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064803 c.1389C>A synonymous_variant 0.4
Rv2752c 3067111 c.-920G>T upstream_gene_variant 0.13
thyA 3074648 c.-177T>G upstream_gene_variant 0.3
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449041 p.Val180Ile missense_variant 0.25
Rv3083 3449046 c.543C>G synonymous_variant 0.29
Rv3083 3449364 c.861C>A synonymous_variant 0.14
Rv3083 3449393 p.Leu297Ser missense_variant 0.17
Rv3083 3449709 c.1206C>G synonymous_variant 0.59
Rv3083 3449968 p.Ala489Thr missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568419 c.261C>T synonymous_variant 0.57
Rv3236c 3612999 p.Gly40Cys missense_variant 0.13
fbiB 3642371 c.837G>T synonymous_variant 0.5
alr 3840425 c.995dupG frameshift_variant 0.13
alr 3840493 c.928C>T synonymous_variant 0.58
alr 3841253 c.168C>T synonymous_variant 0.5
alr 3841349 c.72C>A synonymous_variant 0.3
clpC1 4039161 p.His515Gly missense_variant 0.13
clpC1 4039169 p.Glu512Asp missense_variant 0.36
clpC1 4039691 c.1014G>C synonymous_variant 0.18
clpC1 4039948 p.Gly253* stop_gained 0.13
clpC1 4040057 c.648C>T synonymous_variant 0.27
clpC1 4040246 c.459C>T synonymous_variant 0.33
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4043901 c.381C>T synonymous_variant 0.12
embC 4240207 c.345G>A synonymous_variant 0.45
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241792 p.Ser644Pro missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4243876 p.Leu215Pro missense_variant 0.14
embA 4244845 p.Arg538Pro missense_variant 0.33
embA 4245603 p.Gly791Trp missense_variant 0.5
embA 4245853 p.Ala874Val missense_variant 0.33
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246567 c.54_55insT frameshift_variant 0.4
embB 4247039 p.Phe176Val missense_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248552 p.Ala680Asp missense_variant 0.12
embB 4249053 p.Thr847Asn missense_variant 0.2
aftB 4267431 p.Ser469Leu missense_variant 0.47
aftB 4268639 c.198G>A synonymous_variant 0.4
aftB 4268900 c.-64C>A upstream_gene_variant 0.25
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4326961 c.-588G>C upstream_gene_variant 0.15
ethR 4326964 c.-585G>A upstream_gene_variant 0.2
ethR 4326970 c.-579G>T upstream_gene_variant 0.22
whiB6 4338210 p.Tyr104* stop_gained 0.33
whiB6 4338213 c.309T>G synonymous_variant 0.33
whiB6 4338217 p.Asn102Thr missense_variant 0.33
whiB6 4338343 p.Trp60* stop_gained 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408464 c.-262G>A upstream_gene_variant 0.6