TB-Profiler result

Run: SRR21677887
Summary

Run ID: SRR21677887

Sample name:

Date: 04-04-2023 02:49:28

Number of reads: 123850

Percentage reads mapped: 98.27

Strain: lineage4

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
lineage4 Euro-American LAM;T;S;X;H 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
gyrB 6576 p.Arg446His missense_variant 0.2 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.22 streptomycin
katG 2154476 c.1635delG frameshift_variant 0.4 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 5442 p.Val68Ala missense_variant 1.0
gyrB 5818 c.579G>T synonymous_variant 0.2
gyrB 7167 p.Ala643Val missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8583 p.Asp428Tyr missense_variant 0.2
mshA 576215 p.Leu290Val missense_variant 0.33
mshA 576589 c.1242A>T synonymous_variant 0.17
ccsA 620837 p.Gly316Asp missense_variant 0.5
rpoB 762274 p.Ala823Asp missense_variant 0.29
rpoC 763781 p.Ser138Pro missense_variant 0.22
rpoC 764485 c.1116G>C synonymous_variant 0.5
rpoC 765021 p.Ala551Glu missense_variant 0.33
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776150 p.Met777Ile missense_variant 0.4
mmpL5 777433 p.Ala350Ser missense_variant 1.0
mmpR5 779003 p.Asp5Gly missense_variant 1.0
mmpS5 779632 c.-727G>T upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781703 c.144G>T synonymous_variant 0.4
rpsL 781900 p.Arg114Leu missense_variant 0.67
rplC 800890 p.Val28Met missense_variant 0.29
fbiC 1305460 p.Ala844Thr missense_variant 0.4
embR 1417466 c.-119T>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.29
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.33
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.33
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.29
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.29
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.29
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.29
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.29
rrs 1472688 n.844C>A non_coding_transcript_exon_variant 0.33
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.25
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.22
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.22
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.22
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.22
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.22
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.22
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.18
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.18
rrl 1474363 n.706A>G non_coding_transcript_exon_variant 0.17
rrl 1474736 n.1084delG non_coding_transcript_exon_variant 0.33
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.5
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.33
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.33
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.33
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.33
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.33
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.33
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.5
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.5
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.29
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.29
fabG1 1673162 c.-278T>C upstream_gene_variant 1.0
fabG1 1673629 c.191delA frameshift_variant 0.33
rpsA 1833598 c.57C>T synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102377 c.666A>G synonymous_variant 0.29
katG 2154159 c.1953G>A synonymous_variant 0.4
katG 2154602 p.Gly504Trp missense_variant 0.15
katG 2154881 p.Ala411Ser missense_variant 0.25
katG 2156078 p.Thr12Ser missense_variant 0.25
Rv1979c 2223012 p.Tyr51* stop_gained 0.29
Rv1979c 2223246 c.-82A>G upstream_gene_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859363 c.1056T>C synonymous_variant 0.25
pepQ 2859810 c.609G>T synonymous_variant 0.29
pepQ 2860010 p.Ala137Pro missense_variant 0.17
pepQ 2860092 c.327C>T synonymous_variant 0.25
pepQ 2860216 p.Ala68Glu missense_variant 0.2
pepQ 2860333 p.Asn29Ser missense_variant 0.2
ribD 2986934 p.Tyr32* stop_gained 0.2
Rv2752c 3067134 c.-943C>A upstream_gene_variant 0.22
thyX 3068020 c.-75G>A upstream_gene_variant 0.4
thyA 3074659 c.-188G>T upstream_gene_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448707 c.204G>A synonymous_variant 0.29
Rv3083 3449787 c.1284C>T synonymous_variant 0.82
fprA 3474817 p.Phe271Leu missense_variant 0.33
Rv3236c 3612077 p.Ser347Trp missense_variant 0.22
Rv3236c 3612373 c.744C>A synonymous_variant 0.4
fbiA 3640564 p.Gly8Ser missense_variant 0.5
fbiB 3642527 c.993A>T synonymous_variant 0.4
fbiB 3642881 c.1347A>C stop_lost&splice_region_variant 0.4
ddn 3986748 c.-96G>C upstream_gene_variant 0.4
ddn 3986820 c.-24C>A upstream_gene_variant 0.5
ddn 3987162 p.Leu107Met missense_variant 0.33
clpC1 4039441 p.Arg422Ser missense_variant 0.4
clpC1 4039889 c.816G>T synonymous_variant 0.5
embC 4240433 p.Tyr191His missense_variant 0.33
embC 4240828 c.966G>T synonymous_variant 0.67
embC 4241000 c.1145_1147delCGG disruptive_inframe_deletion 1.0
embA 4243833 p.Ala201Thr missense_variant 0.8
embB 4246930 p.Gln139His missense_variant 1.0
embB 4247609 p.Ser366Thr missense_variant 0.4
embB 4247828 p.Ala439Pro missense_variant 0.22
embB 4249408 c.2895G>A synonymous_variant 0.5
embB 4249536 p.Glu1008Gly missense_variant 0.4
aftB 4267680 p.Ser386Leu missense_variant 0.2
ethA 4326055 c.1419C>A synonymous_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0