Run ID: SRR6045618
Sample name:
Date: 04-04-2023 12:02:30
Number of reads: 1913099
Percentage reads mapped: 70.13
Strain: lineage3.1.2
Drug-resistance: Other
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.99 |
lineage3.1 | East-African-Indian | Non-CAS1-Delhi | RD750 | 1.0 |
lineage3.1.2 | East-African-Indian | CAS;CAS2 | RD750 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.86 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | 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 | 0.23 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.98 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472137 | n.292G>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472151 | n.306C>T | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472160 | n.315C>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472203 | n.358G>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472494 | n.649A>G | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472498 | n.653C>T | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472507 | n.662C>G | non_coding_transcript_exon_variant | 0.62 |
rrs | 1472513 | n.668T>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472517 | n.672T>A | non_coding_transcript_exon_variant | 0.68 |
rrs | 1472518 | n.673G>T | non_coding_transcript_exon_variant | 0.7 |
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.77 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.77 |
rrs | 1472544 | n.699C>A | non_coding_transcript_exon_variant | 0.77 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.77 |
rrs | 1472549 | n.704G>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472566 | n.721G>A | non_coding_transcript_exon_variant | 0.72 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.77 |
rrs | 1472579 | n.734G>C | non_coding_transcript_exon_variant | 0.69 |
rrs | 1472580 | n.735C>T | non_coding_transcript_exon_variant | 0.52 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.88 |
rrs | 1472584 | n.739A>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.78 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.78 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.83 |
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.95 |
rrs | 1472658 | n.813G>A | non_coding_transcript_exon_variant | 0.86 |
rrs | 1472660 | n.815T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.9 |
rrs | 1472668 | n.825_829delGGGTT | non_coding_transcript_exon_variant | 0.94 |
rrs | 1472675 | n.830_831insAGAC | non_coding_transcript_exon_variant | 0.84 |
rrs | 1472680 | n.835C>T | non_coding_transcript_exon_variant | 0.47 |
rrs | 1472681 | n.837_838delTT | non_coding_transcript_exon_variant | 0.83 |
rrs | 1472687 | n.842_843insC | non_coding_transcript_exon_variant | 0.83 |
rrs | 1472690 | n.845C>A | non_coding_transcript_exon_variant | 0.91 |
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.88 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.88 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.83 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.83 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.7 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.63 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472824 | n.979T>A | non_coding_transcript_exon_variant | 0.58 |
rrs | 1472827 | n.982G>T | non_coding_transcript_exon_variant | 0.58 |
rrs | 1472828 | n.983T>C | non_coding_transcript_exon_variant | 0.58 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.24 |
rrs | 1473053 | n.1208T>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473055 | n.1210C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1473081 | n.1236C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473130 | n.1285G>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.13 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474218 | n.561T>A | non_coding_transcript_exon_variant | 0.67 |
rrl | 1474228 | n.571T>C | non_coding_transcript_exon_variant | 0.67 |
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1474674 | n.1018delC | non_coding_transcript_exon_variant | 0.33 |
rrl | 1474677 | n.1020A>G | non_coding_transcript_exon_variant | 0.43 |
rrl | 1474709 | n.1052G>A | non_coding_transcript_exon_variant | 0.4 |
rrl | 1474722 | n.1065T>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1474734 | n.1077G>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1475699 | n.2042C>T | non_coding_transcript_exon_variant | 0.33 |
rrl | 1475704 | n.2047C>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1475713 | n.2056C>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475716 | n.2059A>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475717 | n.2060C>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.23 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.27 |
rrl | 1475906 | n.2249C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475916 | n.2259C>G | non_coding_transcript_exon_variant | 0.23 |
rrl | 1475937 | n.2280A>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1475943 | n.2286G>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475945 | n.2288C>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475952 | n.2295A>G | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475970 | n.2313C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475975 | n.2318C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475977 | n.2320A>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475995 | n.2338G>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475997 | n.2340A>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475998 | n.2341C>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476001 | n.2344T>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476030 | n.2373A>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476126 | n.2469C>T | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476130 | n.2473G>A | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476135 | n.2478T>C | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476141 | n.2484A>G | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476153 | n.2496T>C | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476165 | n.2508T>G | non_coding_transcript_exon_variant | 0.77 |
rrl | 1476194 | n.2537A>G | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476195 | n.2538C>A | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476196 | n.2539C>A | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476200 | n.2543A>T | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476201 | n.2544C>T | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476204 | n.2547C>A | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476210 | n.2553G>T | non_coding_transcript_exon_variant | 0.86 |
rrl | 1476211 | n.2554G>T | non_coding_transcript_exon_variant | 0.86 |
rrl | 1476212 | n.2555T>C | non_coding_transcript_exon_variant | 0.86 |
rrl | 1476214 | n.2557G>C | non_coding_transcript_exon_variant | 0.86 |
rrl | 1476215 | n.2558C>A | non_coding_transcript_exon_variant | 0.86 |
rrl | 1476225 | n.2568T>G | non_coding_transcript_exon_variant | 0.94 |
rrl | 1476227 | n.2570C>T | non_coding_transcript_exon_variant | 0.93 |
rrl | 1476229 | n.2572C>T | non_coding_transcript_exon_variant | 0.94 |
rrl | 1476250 | n.2593C>G | non_coding_transcript_exon_variant | 0.97 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476257 | n.2600G>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476301 | n.2644A>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476302 | n.2645G>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.9 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.87 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.86 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.93 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.89 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.89 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.85 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.83 |
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476524 | n.2867C>A | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.25 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918696 | p.Ala253Pro | missense_variant | 0.96 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168604 | p.Pro670Leu | missense_variant | 0.97 |
Rv1979c | 2223257 | c.-93G>C | upstream_gene_variant | 1.0 |
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 | 0.98 |
eis | 2715432 | c.-100C>T | upstream_gene_variant | 1.0 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3475052 | p.Asn349Thr | missense_variant | 1.0 |
rpoA | 3878552 | c.-45C>A | upstream_gene_variant | 0.22 |
rpoA | 3878567 | c.-60C>G | upstream_gene_variant | 0.5 |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4248241 | c.1728C>G | synonymous_variant | 0.99 |
ethR | 4327693 | p.Asp49Asn | missense_variant | 0.97 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4408147 | p.Ala19Val | missense_variant | 1.0 |