TB-Profiler result

Run: SRR1735569
Summary

Run ID: SRR1735569

Sample name:

Date: 03-04-2023 17:57:21

Number of reads: 374729

Percentage reads mapped: 98.98

Strain: La3

Drug-resistance: HR-TB

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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
La3 M.orygis None 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
katG 2155105 c.1006delC frameshift_variant 0.33 isoniazid
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 5929 c.690G>A synonymous_variant 1.0
gyrB 6109 c.870G>A synonymous_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrB 6717 p.Ile493Thr missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490661 c.-122_-121insGCGAGC upstream_gene_variant 1.0
fgd1 491150 p.Pro123Leu missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491749 p.Leu323Phe missense_variant 1.0
rpoB 759786 c.-21G>T upstream_gene_variant 0.25
rpoB 762027 p.Leu741Ile missense_variant 0.25
rpoB 762352 c.2557_2562dupGACGAG conservative_inframe_insertion 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764343 p.Arg325His missense_variant 0.67
rpoC 764352 p.Val328Ala missense_variant 0.67
rpoC 764600 p.Gly411Ser missense_variant 0.17
rpoC 765195 p.Thr609Ile missense_variant 0.22
rpoC 765960 p.Ala864Val missense_variant 0.22
rpoC 766807 c.3438T>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775651 p.Arg944Trp missense_variant 0.22
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778086 c.394dupG frameshift_variant 1.0
mmpS5 779625 c.-723_-721delTTG upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304740 p.Gly604Ser missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 1.0
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 1.0
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 1.0
rrl 1476518 n.2861G>A non_coding_transcript_exon_variant 1.0
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 1.0
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 1.0
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 1.0
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 1.0
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 1.0
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 1.0
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 1.0
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 1.0
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 1.0
inhA 1673680 c.-522C>G upstream_gene_variant 1.0
rpsA 1834363 c.822G>A synonymous_variant 1.0
rpsA 1834772 p.Arg411Ser missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.43
katG 2154707 p.Val469Leu missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156164 c.-53G>T upstream_gene_variant 0.4
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168035 p.Thr860Ala missense_variant 0.4
PPE35 2169279 c.1312_1333delAACAATGGTGTCTTTTACCGTG frameshift_variant 1.0
PPE35 2169409 c.1197_1203delGGGTACC frameshift_variant 0.33
PPE35 2170669 c.-57G>A upstream_gene_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289317 c.-77delG upstream_gene_variant 0.29
pncA 2289978 c.-737T>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714698 c.634dupC frameshift_variant 0.2
eis 2714879 p.Asp152Asn missense_variant 0.29
ahpC 2726338 p.Val49Gly missense_variant 1.0
ahpC 2726378 c.186T>A synonymous_variant 1.0
folC 2747206 c.393G>C synonymous_variant 1.0
Rv2752c 3067009 c.-818A>G upstream_gene_variant 1.0
thyX 3067812 p.Gln45Arg missense_variant 1.0
thyA 3074069 p.Val135Phe missense_variant 0.17
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474229 p.Arg75Cys missense_variant 0.2
fprA 3474394 p.Gly130Ser missense_variant 0.18
fprA 3475113 c.1107G>A synonymous_variant 0.94
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475323 c.1317T>C synonymous_variant 1.0
Rv3236c 3612694 c.423T>C synonymous_variant 1.0
fbiB 3641584 p.Val17Ala missense_variant 1.0
ddn 3987122 p.Lys93Asn missense_variant 0.22
clpC1 4039853 c.852G>A synonymous_variant 1.0
embC 4240648 c.786C>T synonymous_variant 0.43
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242952 c.-281T>G upstream_gene_variant 0.43
embC 4243079 p.Ala1073Thr missense_variant 1.0
embA 4243451 c.219G>A synonymous_variant 0.18
embA 4244154 p.Thr308Ala missense_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247533 p.Met340Ile missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249049 p.Gly846Ser missense_variant 0.12
aftB 4266976 p.Pro621Thr missense_variant 0.2
aftB 4268548 c.289C>T synonymous_variant 0.29
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327042 p.Asp144Asn missense_variant 1.0
ethR 4327210 c.-339G>C upstream_gene_variant 0.33
ethA 4328211 c.-738A>G upstream_gene_variant 1.0
whiB6 4338269 p.Gly85Ser missense_variant 1.0
whiB6 4338516 c.5_6insCTTCCCGCCCCGACAGCCTGGGCCGACCCGTCGGTTAATGCG disruptive_inframe_insertion 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0