TB-Profiler result

Run: SRR1062863
Summary

Run ID: SRR1062863

Sample name:

Date: 02-04-2023 18:37:22

Number of reads: 2548767

Percentage reads mapped: 44.24

Strain: lineage1.2.2.1

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
lineage1 Indo-Oceanic EAI RD239 0.98
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.93
lineage1.2.2.1 Indo-Oceanic NA RD239 0.96
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 5075 c.-165C>T upstream_gene_variant 0.99
gyrB 6112 p.Met291Ile missense_variant 0.98
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.97
gyrA 9143 c.1842T>C synonymous_variant 0.98
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491060 p.Met93Thr missense_variant 0.95
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620659 p.Arg257Cys missense_variant 0.97
rpoC 763031 c.-339T>C upstream_gene_variant 0.97
rpoC 763884 p.Ala172Val missense_variant 0.91
rpoC 763886 c.517C>A synonymous_variant 0.94
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800899 p.Ala31Thr missense_variant 0.97
embR 1417019 p.Cys110Tyr missense_variant 0.92
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 0.94
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.17
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.26
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.27
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.29
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.32
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.38
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.37
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.37
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.36
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.35
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.36
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.39
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.3
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.2
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.13
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.13
rrs 1472222 n.377G>A non_coding_transcript_exon_variant 0.13
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.13
rrs 1472229 n.384C>T non_coding_transcript_exon_variant 0.13
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.13
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.13
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.13
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.27
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.26
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.23
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.51
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.51
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.51
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.51
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.52
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.51
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.54
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.56
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.48
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.13
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.46
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.51
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.67
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.71
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.72
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.7
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.24
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.13
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.14
rrs 1473008 n.1164delT non_coding_transcript_exon_variant 0.12
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.34
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.36
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.36
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.36
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.35
rrs 1473080 n.1235C>A non_coding_transcript_exon_variant 0.36
rrs 1473091 n.1246G>A non_coding_transcript_exon_variant 0.35
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.28
rrs 1473099 n.1254T>G non_coding_transcript_exon_variant 0.28
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.28
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.41
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.44
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.47
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.46
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.45
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.46
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.47
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.55
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.57
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.58
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.57
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.59
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.62
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.62
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.55
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.54
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.45
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.46
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.41
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.4
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.32
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.24
rrl 1474928 n.1271C>A non_coding_transcript_exon_variant 0.12
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.15
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.18
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.39
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.4
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.51
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.51
rrl 1475869 n.2212C>T non_coding_transcript_exon_variant 0.48
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.45
rrl 1475880 n.2223C>G non_coding_transcript_exon_variant 0.41
rrl 1475881 n.2224T>G non_coding_transcript_exon_variant 0.41
rrl 1475882 n.2225C>G non_coding_transcript_exon_variant 0.41
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.41
rrl 1475897 n.2240T>G non_coding_transcript_exon_variant 0.39
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.3
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.23
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.34
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.4
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.41
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.41
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.42
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.42
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.42
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.42
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.42
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.43
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.42
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.44
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.66
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.72
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.74
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.75
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.76
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.76
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.81
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.79
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.79
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.79
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.73
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.73
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.58
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.43
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.4
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.4
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.4
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.41
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.42
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.42
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.42
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.42
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.41
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.39
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.33
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.25
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.98
Rv1979c 2222308 p.Asp286Gly missense_variant 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.94
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
thyX 3068115 c.-170C>T upstream_gene_variant 0.94
thyA 3074034 c.438T>C synonymous_variant 0.95
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.93
fprA 3474679 p.Ile225Val missense_variant 0.98
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 0.98
embC 4240671 p.Thr270Ile missense_variant 0.96
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.96
embB 4247646 p.Glu378Ala missense_variant 0.98
aftB 4268852 c.-16G>A upstream_gene_variant 0.98
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 0.96
ethA 4326439 p.Asn345Lys missense_variant 0.98
ethR 4327450 c.-99G>A upstream_gene_variant 0.92
whiB6 4338215 p.Gly103Cys missense_variant 0.96
whiB6 4338374 p.Lys50Glu missense_variant 0.95
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.93
gid 4407873 c.330G>T synonymous_variant 0.97