TB-Profiler result

Run: SRR3675463
Summary

Run ID: SRR3675463

Sample name:

Date: 04-04-2023 05:28:43

Number of reads: 455187

Percentage reads mapped: 75.28

Strain:

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
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 5682 p.Gln148Arg missense_variant 0.67
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8562 p.Leu421Met missense_variant 0.5
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620864 c.974G>T stop_lost&splice_region_variant 0.18
rpoB 760269 p.Thr155Ala missense_variant 0.67
rpoB 760523 p.Ser239Arg missense_variant 0.4
rpoB 761385 p.Ala527Ser missense_variant 0.4
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762757 p.Ser984* stop_gained 0.67
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764374 p.Phe335Leu missense_variant 0.4
rpoC 764767 c.1398G>T synonymous_variant 0.2
rpoC 766879 c.3510G>T synonymous_variant 0.5
rpoC 766984 c.3615G>T synonymous_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775690 p.Ala931Ser missense_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776864 p.Met539Ile missense_variant 0.12
mmpL5 777076 p.Ala469Ser missense_variant 0.17
mmpL5 777237 p.Tyr415Phe missense_variant 0.14
mmpL5 777907 p.Leu192Met missense_variant 0.22
mmpL5 777920 c.561C>A synonymous_variant 0.22
mmpL5 778265 p.Met72Ile missense_variant 0.25
mmpL5 779376 c.-896C>A upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781526 c.-34G>T upstream_gene_variant 0.29
fbiC 1303848 p.Phe306Leu missense_variant 0.18
fbiC 1305492 c.2562T>C synonymous_variant 0.22
Rv1258c 1406543 c.798G>A synonymous_variant 1.0
Rv1258c 1406767 p.Gln192* stop_gained 0.18
embR 1416859 c.489C>A synonymous_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.5
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.67
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.8
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.67
rrs 1472677 n.833_834delTT non_coding_transcript_exon_variant 0.67
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.67
rrs 1472683 n.839_842delGGGA non_coding_transcript_exon_variant 0.67
rrs 1472690 n.845C>G non_coding_transcript_exon_variant 0.67
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.57
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.57
rrs 1472726 n.881G>A non_coding_transcript_exon_variant 0.44
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.4
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.4
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.36
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.36
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.36
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.22
rrs 1472778 n.933C>T non_coding_transcript_exon_variant 0.22
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.67
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.67
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.67
rrs 1472967 n.1122G>T non_coding_transcript_exon_variant 0.5
rrs 1472969 n.1125_1126delCG non_coding_transcript_exon_variant 0.5
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.5
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.5
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.5
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.5
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.5
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.5
rrs 1473000 n.1155G>A non_coding_transcript_exon_variant 0.67
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.67
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.5
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.4
rrs 1473010 n.1165C>T non_coding_transcript_exon_variant 0.4
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.4
rrl 1475152 n.1495G>T non_coding_transcript_exon_variant 1.0
rrl 1475475 n.1818C>A non_coding_transcript_exon_variant 0.18
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.67
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.67
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.67
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.55
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.55
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.55
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.58
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.69
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.69
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.69
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.73
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.57
rrl 1476518 n.2861G>A non_coding_transcript_exon_variant 0.67
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.67
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.67
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.67
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.8
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
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 1.0
fabG1 1673346 c.-94C>A upstream_gene_variant 0.29
inhA 1674653 p.Pro151Gln missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102014 c.1029C>A synonymous_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168266 p.Gly783Arg missense_variant 0.4
PPE35 2170048 p.Leu189Val missense_variant 0.2
PPE35 2170053 p.Thr187Ser missense_variant 0.2
PPE35 2170444 p.Trp57Arg missense_variant 0.17
Rv1979c 2222781 c.384C>A synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289630 c.-389G>A upstream_gene_variant 0.4
kasA 2517953 c.-162C>A upstream_gene_variant 0.15
kasA 2518232 p.Glu40* stop_gained 0.29
kasA 2518811 p.Asp233Tyr missense_variant 0.17
kasA 2519258 p.Leu382Ile missense_variant 0.33
eis 2715469 c.-137T>A upstream_gene_variant 0.22
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747484 p.Pro39Thr missense_variant 0.43
pepQ 2859988 p.Arg144Leu missense_variant 0.25
pepQ 2860539 c.-121G>T upstream_gene_variant 0.15
ribD 2986842 p.Pro2Ser missense_variant 0.12
thyA 3074645 c.-174T>G upstream_gene_variant 0.75
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087025 c.209delT frameshift_variant 0.29
fbiD 3339273 c.156T>G synonymous_variant 0.36
Rv3083 3448466 c.-38G>A upstream_gene_variant 0.18
fprA 3473886 c.-120delA upstream_gene_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474516 c.510C>A synonymous_variant 0.33
fprA 3475026 c.1020C>T synonymous_variant 0.2
whiB7 3568660 p.Pro7Leu missense_variant 1.0
Rv3236c 3612658 c.459G>T synonymous_variant 0.5
Rv3236c 3612678 p.Glu147* stop_gained 0.4
alr 3840674 p.Asp249Glu missense_variant 0.12
alr 3840846 p.Gly192Ala missense_variant 0.83
clpC1 4038489 p.Ala739Asp missense_variant 0.4
clpC1 4039658 p.Glu349Asp missense_variant 0.4
panD 4044318 c.-37G>T upstream_gene_variant 0.18
embC 4240055 p.Gly65Cys missense_variant 0.5
embC 4240501 p.Ser213Arg missense_variant 0.33
embC 4241879 p.Leu673Met missense_variant 0.14
embC 4241889 p.Ala676Glu missense_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243052 p.Thr1064Ser missense_variant 0.29
embB 4246160 c.-354G>T upstream_gene_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4247449 p.His312Gln missense_variant 0.29
embB 4247455 c.942C>A synonymous_variant 0.25
embB 4247571 p.Pro353Gln missense_variant 0.29
embB 4247576 c.1063_1064insA frameshift_variant 0.29
aftB 4267428 p.Ser470Leu missense_variant 0.15
aftB 4268223 p.Arg205Gln missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407532 p.Ala224Glu missense_variant 0.2
gid 4407588 c.615A>G synonymous_variant 1.0