TB-Profiler result

Run: SRR13837514
Summary

Run ID: SRR13837514

Sample name:

Date: 03-04-2023 09:12:12

Number of reads: 593220

Percentage reads mapped: 97.92

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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 5922 p.Glu228Gly missense_variant 1.0
gyrB 7242 p.Lys668Thr missense_variant 1.0
gyrA 7532 c.231T>C synonymous_variant 0.13
gyrA 7541 c.240C>G synonymous_variant 0.12
gyrA 7571 c.270G>C synonymous_variant 0.18
gyrA 7607 c.306C>G synonymous_variant 0.11
gyrA 7694 c.393A>G synonymous_variant 0.12
gyrA 7710 c.409T>C synonymous_variant 0.12
gyrA 7715 c.414G>C synonymous_variant 0.11
gyrA 7728 c.427_429delAGGinsCGC synonymous_variant 0.17
gyrA 7760 c.459C>T synonymous_variant 0.17
gyrA 7763 c.462T>C synonymous_variant 0.18
gyrA 7799 c.498A>G synonymous_variant 0.16
gyrA 7835 c.534A>G synonymous_variant 0.12
gyrA 7838 c.537C>G synonymous_variant 0.11
ccsA 620360 p.Tyr157Ser missense_variant 1.0
rpoB 760805 c.999G>C synonymous_variant 0.14
rpoB 760820 c.1014T>C synonymous_variant 0.11
rpoB 760826 c.1020C>G synonymous_variant 0.12
rpoB 760830 c.1024T>C synonymous_variant 0.12
rpoB 760845 p.Thr347Pro missense_variant 0.12
rpoB 760859 c.1053T>C synonymous_variant 0.12
rpoB 760919 c.1113C>G synonymous_variant 0.14
rpoB 760925 c.1119T>C synonymous_variant 0.13
rpoB 760928 c.1122G>C synonymous_variant 0.13
rpoB 760934 c.1128C>T synonymous_variant 0.14
rpoB 761356 c.1550_1551insA frameshift_variant 1.0
rpoB 761690 c.1884G>C synonymous_variant 0.12
rpoC 763347 c.-23C>G upstream_gene_variant 1.0
rpoC 763402 c.33C>G synonymous_variant 0.11
rpoC 763414 c.45T>C synonymous_variant 0.11
rpoC 766025 p.Val886Met missense_variant 1.0
rpoC 766363 c.2994G>C synonymous_variant 0.11
rpoC 766447 c.3078T>C synonymous_variant 0.17
mmpL5 776145 p.Ala779Gly missense_variant 1.0
mmpL5 776954 p.Lys509Asn missense_variant 1.0
rplC 801231 c.423C>A synonymous_variant 1.0
atpE 1460916 c.-129G>A upstream_gene_variant 1.0
rrs 1472756 n.911A>C non_coding_transcript_exon_variant 0.18
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.14
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.14
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.12
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.12
rrl 1476201 n.2544C>G non_coding_transcript_exon_variant 1.0
katG 2155137 c.975G>C synonymous_variant 1.0
PPE35 2168892 p.Thr574Lys missense_variant 1.0
Rv1979c 2222852 p.Ala105Thr missense_variant 1.0
ribD 2987259 p.Leu141Val missense_variant 1.0
Rv2752c 3065161 p.Asn344Thr missense_variant 1.0
Rv2752c 3065830 p.Ile121Thr missense_variant 0.93
Rv2752c 3067100 c.-909G>A upstream_gene_variant 1.0
thyA 3074076 c.396C>G synonymous_variant 0.12
thyA 3074106 c.366T>C synonymous_variant 0.13
thyA 3074117 c.355C>T synonymous_variant 0.12
thyA 3074120 c.352T>C synonymous_variant 0.12
thyA 3074130 c.342G>C synonymous_variant 0.13
thyA 3074157 c.315C>G synonymous_variant 0.13
thyA 3074160 c.312A>G synonymous_variant 0.13
thyA 3074163 p.Ala103Thr missense_variant 0.13
thyA 3074172 c.300G>C synonymous_variant 0.12
thyA 3074205 p.Glu89Asp missense_variant 0.11
fbiD 3339117 c.-1C>T upstream_gene_variant 1.0
Rv3083 3448661 p.Val53Ala missense_variant 1.0
Rv3236c 3612041 p.Val359Glu missense_variant 1.0
fbiA 3640418 c.-125C>A upstream_gene_variant 1.0
rpoA 3877877 p.Ala211Ser missense_variant 1.0
ddn 3986699 c.-145C>G upstream_gene_variant 0.12
clpC1 4038398 c.2307G>T synonymous_variant 0.11
clpC1 4038530 p.Glu725Asp missense_variant 0.12
clpC1 4039250 c.1455C>G synonymous_variant 0.92
embC 4242113 c.2251C>T synonymous_variant 1.0
embB 4246367 c.-147C>T upstream_gene_variant 1.0
whiB6 4338567 c.-46C>T upstream_gene_variant 0.96
gid 4408302 c.-101delC upstream_gene_variant 1.0