TB-Profiler result

Run: SRR6855867
Summary

Run ID: SRR6855867

Sample name:

Date: 04-04-2023 17:48:21

Number of reads: 475537

Percentage reads mapped: 98.67

Strain: lineage4.3.2.1;lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.87
lineage4 Euro-American LAM;T;S;X;H None 0.16
lineage4.3 Euro-American (LAM) mainly-LAM None 0.07
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.83
lineage4.3.2 Euro-American (LAM) LAM3 None 0.09
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.85
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.1
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 5665 p.Asp142Glu missense_variant 0.12
gyrA 7222 c.-80C>T upstream_gene_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575209 c.-139G>A upstream_gene_variant 0.13
mshA 575819 p.Ser158Thr missense_variant 0.22
mshA 575907 p.Ala187Val missense_variant 0.64
mshA 576355 c.1008G>A synonymous_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 0.69
rpoB 760077 p.Glu91* stop_gained 0.12
rpoB 760409 c.603C>T synonymous_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 0.68
rpoC 764995 c.1626C>G synonymous_variant 0.23
rpoC 766266 p.Leu966Gln missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.67
mmpL5 776182 p.Asp767Asn missense_variant 0.82
mmpL5 777798 p.Thr228Met missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 0.9
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303751 p.Leu274* stop_gained 0.11
fbiC 1303997 p.Gly356Val missense_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407466 c.-126G>A upstream_gene_variant 0.11
embR 1416992 p.Lys119Thr missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.17
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.18
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.18
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.15
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.15
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.15
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.14
rrs 1472671 n.826G>A non_coding_transcript_exon_variant 0.14
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.13
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.13
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.13
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.14
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.13
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.11
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.1
rrl 1475262 n.1607_1615delGGTGTGGAG non_coding_transcript_exon_variant 0.12
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.11
rrl 1476598 n.2941C>A non_coding_transcript_exon_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 0.68
rpsA 1834281 p.His247Arg missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103226 c.-184C>G upstream_gene_variant 0.63
katG 2154724 p.Arg463Leu missense_variant 0.93
katG 2155772 p.Arg114Cys missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 0.78
PPE35 2168344 p.Gly757Arg missense_variant 0.29
PPE35 2169800 c.812delA frameshift_variant 0.13
Rv1979c 2222145 p.Leu340Phe missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289877 c.-636C>T upstream_gene_variant 0.12
kasA 2518515 p.Pro134His missense_variant 0.29
kasA 2519176 c.1062G>A synonymous_variant 0.12
kasA 2519285 p.Tyr391His missense_variant 0.12
eis 2714619 c.714C>T synonymous_variant 0.1
eis 2715378 c.-46A>G upstream_gene_variant 0.11
ahpC 2726389 p.Ala66Val missense_variant 0.11
pepQ 2859929 p.Arg164Trp missense_variant 0.11
ribD 2986859 c.21C>T synonymous_variant 0.11
Rv2752c 3065543 p.Glu217Lys missense_variant 0.12
Rv2752c 3067147 c.-956A>G upstream_gene_variant 0.15
thyX 3067586 c.360C>A synonymous_variant 0.2
thyX 3067622 c.324C>T synonymous_variant 0.22
thyA 3073868 p.Thr202Ala missense_variant 0.3
ald 3086739 c.-81G>A upstream_gene_variant 0.88
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087829 p.Pro337Leu missense_variant 0.11
Rv3083 3448374 c.-130A>G upstream_gene_variant 0.15
Rv3083 3448555 p.Gly18Arg missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.83
Rv3236c 3613061 p.Ala19Val missense_variant 0.13
ddn 3986685 c.-159T>A upstream_gene_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 0.17
clpC1 4039718 c.987C>T synonymous_variant 0.12
embC 4240204 c.342T>A synonymous_variant 0.14
embC 4240581 p.Leu240His missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244759 c.1529delA frameshift_variant 0.14
embA 4246045 p.Val938Gly missense_variant 0.11
embB 4246537 c.28delA frameshift_variant 0.11
embB 4248860 p.Val783Ile missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 0.88
aftB 4267681 c.1155delG frameshift_variant 0.12
aftB 4268262 p.Ile192Thr missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.76
gid 4407609 c.594G>A synonymous_variant 0.12
gid 4407927 p.Glu92Asp missense_variant 0.93
gid 4408156 p.Leu16Arg missense_variant 0.12