TB-Profiler result

Run: SRR6046115
Summary

Run ID: SRR6046115

Sample name:

Date: 04-04-2023 12:11:34

Number of reads: 588136

Percentage reads mapped: 65.23

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 0.99
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 6932 p.Gln565Lys missense_variant 0.17
gyrB 7106 p.Glu623Lys missense_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
fgd1 491027 p.Asn82Thr missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575424 p.Arg26His missense_variant 1.0
mshA 576089 c.750_769delTGATCGGCGCGCGGCCCGGG frameshift_variant 0.25
ccsA 619831 c.-60T>G upstream_gene_variant 0.3
ccsA 620748 c.858T>G synonymous_variant 0.35
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763321 p.Ala1172Val missense_variant 0.12
rpoC 763456 c.87A>G synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776018 c.2463G>C synonymous_variant 0.13
mmpL5 776021 c.2460G>C synonymous_variant 0.13
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777692 c.789C>T synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801229 p.Ala141Pro missense_variant 0.18
fbiC 1304136 c.1206C>G synonymous_variant 0.33
fbiC 1304524 p.Ala532Thr missense_variant 0.22
fbiC 1304694 c.1764A>T synonymous_variant 0.12
Rv1258c 1406235 p.Pro369Gln missense_variant 0.12
embR 1416781 c.567A>C synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.22
rrl 1475879 n.2222T>C non_coding_transcript_exon_variant 0.5
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 1.0
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 1.0
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.5
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 1.0
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 1.0
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 1.0
rrl 1475897 n.2240T>G non_coding_transcript_exon_variant 1.0
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 1.0
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.5
rrl 1475900 n.2243A>C non_coding_transcript_exon_variant 1.0
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 1.0
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.5
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.5
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 1.0
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 1.0
rrl 1475937 n.2280A>G non_coding_transcript_exon_variant 1.0
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 1.0
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 1.0
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 1.0
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 1.0
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.5
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.5
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.5
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.5
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.4
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.6
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.4
fabG1 1674076 p.Thr213Pro missense_variant 0.33
rpsA 1834025 p.Gln162Lys missense_variant 0.14
rpsA 1834180 p.Lys213Asn missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918138 p.Ala67Thr missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167859 c.2754T>G synonymous_variant 0.21
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289913 c.-672T>C upstream_gene_variant 0.13
pncA 2290147 c.-906T>C upstream_gene_variant 0.25
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.33
folC 2746212 p.Arg463Gly missense_variant 0.12
folC 2746525 c.1074G>A synonymous_variant 0.17
folC 2747689 c.-91C>T upstream_gene_variant 0.18
ribD 2986659 c.-180G>A upstream_gene_variant 0.12
Rv2752c 3064877 p.Ser439Thr missense_variant 0.2
Rv2752c 3065948 p.Gly82Trp missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473998 c.-9G>A upstream_gene_variant 1.0
fprA 3473998 c.-10_-9insA upstream_gene_variant 1.0
fprA 3474655 p.Asp217His missense_variant 0.15
Rv3236c 3612190 c.927G>A synonymous_variant 0.15
fbiA 3641426 p.His295Arg missense_variant 0.11
fbiB 3641766 p.Ile78Val missense_variant 0.11
fbiB 3642877 p.Lys448Arg missense_variant 1.0
alr 3840956 c.465C>T synonymous_variant 0.12
clpC1 4040241 p.Thr155Phe missense_variant 0.33
clpC1 4040249 p.Glu152Gly missense_variant 0.29
embC 4241050 c.1188T>G synonymous_variant 0.13
embC 4241077 c.1215C>T synonymous_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244424 p.Arg398Trp missense_variant 0.22
embA 4245077 c.1845G>C synonymous_variant 0.15
embB 4247981 c.1468C>T synonymous_variant 1.0
embB 4248578 p.Ala689Thr missense_variant 0.11
embB 4248627 p.Ala705Val missense_variant 0.13
aftB 4267747 p.Ser364Pro missense_variant 0.13
ethA 4327472 c.2T>C start_lost 0.13
ethA 4328471 c.-998A>G upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0