TB-Profiler result

Run: SRR1791910
Summary

Run ID: SRR1791910

Sample name:

Date: 03-04-2023 18:34:29

Number of reads: 169627

Percentage reads mapped: 21.0

Strain:

Drug-resistance: Other

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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
La1.8.1 M.bovis 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
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide
ethA 4326419 c.1054delG frameshift_variant 0.5 ethionamide, ethionamide
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 5220 c.-20C>A upstream_gene_variant 0.25
gyrB 5752 c.513G>A synonymous_variant 1.0
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8151 p.Ile284Val missense_variant 0.29
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.33
rpoB 760790 c.984C>T synonymous_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764134 c.765C>T synonymous_variant 0.2
rpoC 764869 c.1500C>T synonymous_variant 0.33
rpoC 764872 c.1503A>G synonymous_variant 0.33
rpoC 764875 c.1506C>G synonymous_variant 0.33
rpoC 764878 c.1509C>G synonymous_variant 0.33
rpoC 764887 c.1518G>T synonymous_variant 0.33
rpoC 764902 c.1533C>G synonymous_variant 0.29
rpoC 764911 c.1542A>G synonymous_variant 0.29
rpoC 764912 p.Met515Val missense_variant 0.29
rpoC 764918 p.Val517Ile missense_variant 0.25
rpoC 764935 c.1566T>C synonymous_variant 0.22
rpoC 764944 c.1575C>T synonymous_variant 0.22
rpoC 764948 c.1579T>C synonymous_variant 0.22
rpoC 764953 c.1584G>C synonymous_variant 0.22
rpoC 764956 c.1587T>C synonymous_variant 0.22
rpoC 764958 p.Glu530Ala missense_variant 0.22
rpoC 764968 c.1599T>C synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775799 c.2682G>A synonymous_variant 0.22
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781679 c.120C>G synonymous_variant 0.2
rpsL 781682 c.123T>G synonymous_variant 0.2
rpsL 781703 c.144G>A synonymous_variant 0.22
rpsL 781706 c.147T>G synonymous_variant 0.22
rpsL 781709 c.150G>T synonymous_variant 0.2
rplC 801129 c.321C>A synonymous_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.29
atpE 1461087 p.Leu15Met missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.18
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.14
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.14
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.15
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.15
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.15
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.17
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.17
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.17
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.17
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.17
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.14
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.15
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.31
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.33
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.33
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.36
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.2
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.2
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.18
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.22
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.22
rrs 1472972 n.1127T>A non_coding_transcript_exon_variant 0.18
rrs 1472974 n.1130_1133delTGGT non_coding_transcript_exon_variant 0.18
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.18
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.25
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.23
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.31
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.31
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.31
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.31
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.38
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.29
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.17
rrs 1473054 n.1209C>G non_coding_transcript_exon_variant 0.17
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.25
rrl 1474221 n.564T>C non_coding_transcript_exon_variant 0.25
rrl 1474228 n.571T>A non_coding_transcript_exon_variant 0.25
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.25
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.12
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.24
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.2
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.31
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.31
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.38
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.38
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.38
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.41
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.39
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.39
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.41
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.41
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.41
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.47
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.47
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.43
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.46
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.38
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.38
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.43
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.43
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.43
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.38
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.38
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.3
rpsA 1833675 p.Lys45Arg missense_variant 0.17
rpsA 1833683 p.Arg48Trp missense_variant 0.17
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917865 c.-74_-73delCG upstream_gene_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101865 p.Trp393* stop_gained 0.5
ndh 2102193 p.Arg284Trp missense_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2169895 p.Gly240Ser missense_variant 0.33
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714566 p.Leu256Pro missense_variant 0.33
thyX 3067655 c.291G>A synonymous_variant 0.12
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
Rv3083 3449741 p.Met413Arg missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568792 c.-113C>T upstream_gene_variant 0.18
alr 3841427 c.-7C>T upstream_gene_variant 0.22
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4040021 c.684A>G synonymous_variant 0.22
clpC1 4040032 p.Val225Ile missense_variant 0.22
clpC1 4040033 c.672G>C synonymous_variant 0.22
clpC1 4040036 c.669C>G synonymous_variant 0.22
clpC1 4040051 c.654C>G synonymous_variant 0.2
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4242527 p.Gly889Trp missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242929 p.Pro1023Thr missense_variant 0.4
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 1.0
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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0