Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 833,933 C→T 32.7% D797D (GAC→GAT)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE833,9330CT32.7% 124.0 / 80.3 101D797D (GAC→GAT) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (36/32);  new base T (20/13);  total (56/45)
Fisher's exact test for biased strand distribution p-value = 5.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 110 total aligned reads displayed.

CCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCGGTCGATCCGGCCTGGGAAG  >  minE/833864‑834000
                                                                     |                                                                   
ccGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                                                    >  1:3799207/1‑71 (MQ=255)
ccGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                                                    >  1:3333857/1‑71 (MQ=255)
ccGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                                                    >  1:3290762/1‑71 (MQ=255)
ccGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                                                    >  1:1729023/1‑71 (MQ=255)
ccGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                                                    >  1:5451873/1‑71 (MQ=255)
ccGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGCCGACCTGGTACGAAAAAGACGACa                                                                    >  1:3451766/1‑71 (MQ=255)
 cGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                                                    >  1:590478/1‑70 (MQ=255)
         gAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                                                    >  1:3676956/1‑62 (MQ=255)
         gAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                                                    >  1:2271004/1‑62 (MQ=255)
         gAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                                                    >  1:460371/1‑62 (MQ=255)
         gAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                                                    >  1:4517095/1‑62 (MQ=255)
          aGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTc                                                          >  1:5319269/1‑71 (MQ=255)
           gCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCg                                                         >  1:2561185/1‑71 (MQ=255)
                 gTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATg                                                   >  1:5295264/1‑71 (MQ=255)
                  tctcTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATAc                                                             >  1:4163088/1‑60 (MQ=255)
                      tATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCa                                                 <  1:2424132/68‑1 (MQ=255)
                      tATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATcc                                              >  1:2999031/1‑71 (MQ=255)
                        ttCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCg                                             <  1:3539171/70‑1 (MQ=255)
                        ctCCGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGaa                                                                >  1:1923086/2‑51 (MQ=255)
                        ctCCGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGt                                            >  1:141150/2‑71 (MQ=255)
                         tCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGc                                                  >  1:3065344/1‑64 (MQ=255)
                          ccGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGaa                                                                >  1:2381677/1‑49 (MQ=255)
                          ccGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGtt                                           <  1:5072479/70‑1 (MQ=255)
                           cGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTa                                         >  1:4247396/1‑71 (MQ=255)
                           cGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTa                                         >  1:2743258/1‑71 (MQ=255)
                            gatatcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTa                                         <  1:1043388/67‑1 (MQ=255)
                            gatatcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTAt                                        >  1:892632/4‑71 (MQ=255)
                            gatatcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTAt                                        >  1:892630/4‑71 (MQ=255)
                            gatatcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTAt                                        >  1:3568848/4‑71 (MQ=255)
                            gatatcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTAt                                        >  1:3897985/4‑71 (MQ=255)
                             aCATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATa                                                              >  1:1793678/1‑48 (MQ=255)
                             aCATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTa                                         >  1:426848/1‑69 (MQ=255)
                               atcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGata                                                     >  1:4274569/1‑55 (MQ=255)
                               atcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGata                                                     >  1:3466423/1‑55 (MQ=255)
                               atcgtTCTGCCCACCGCCACCTGCTACGAAAAAGACGATATGaa                                                                >  1:4673438/1‑44 (MQ=12)
                                 catTTTGCCGACGGCGACCTGGTACGAAAAAGAAGACATGAATACTTCGGATATGCATCCGTTTATTCAcc                                   >  1:2473935/1‑71 (MQ=255)
                                 caatttGCCGACGGCGACCTGGTACGAAAAAGACTACATGAATACTTCGGATATGCATCCGTTTATTCAcc                                   >  1:1915154/4‑71 (MQ=255)
                                  atTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCg                                                         <  1:1370847/48‑1 (MQ=255)
                                  atTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGa                                                       <  1:4351762/50‑1 (MQ=255)
                                  atTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCAccc                                  >  1:1279436/1‑71 (MQ=255)
                                    tttGCCGACGGCGACCTGGTACGAAAAAGACGACATGaa                                                                <  1:4593526/39‑1 (MQ=255)
                                       gCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTg                              <  1:3934286/70‑1 (MQ=255)
                                        ccGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGata                                                     <  1:269858/46‑1 (MQ=255)
                                           aCGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGata                                                     <  1:2219525/43‑1 (MQ=255)
                                            cGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTgcg                        >  1:182574/1‑71 (MQ=255)
                                             tgCGACGTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGtt                                           <  1:5074128/50‑1 (MQ=255)
                                             ggCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGtt                                           <  1:3505476/51‑1 (MQ=255)
                                              gCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTgcggc                      <  1:4778080/71‑1 (MQ=255)
                                              gCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTgcggc                      <  1:2071345/71‑1 (MQ=255)
                                               cGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTg                              <  1:1610348/62‑1 (MQ=255)
                                                gACCTGGTACGAAAAAGACGACATGAATACTTCGGata                                                     <  1:1009580/38‑1 (MQ=255)
                                                gACCTGGTACGAAAAAGACGACATGAATACTTCGGata                                                     <  1:3961289/38‑1 (MQ=255)
                                                  ccTGGTACGAAAAAGACGACATGAATACTTCGGata                                                     >  1:1804533/1‑36 (MQ=255)
                                                   cTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGtt                                           <  1:3418381/45‑1 (MQ=255)
                                                   cTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGtt                                           <  1:1536267/45‑1 (MQ=255)
                                                   cTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGtt                                           <  1:1961068/45‑1 (MQ=255)
                                                   cTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGtt                                           <  1:2369790/45‑1 (MQ=255)
                                                   cTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTATTCATCCGCTTTCTGCGGCGGTc                  >  1:3764463/1‑70 (MQ=255)
                                                   cTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTATTCATCCGCTTTCTGCGGCGGTCg                 <  1:495935/71‑1 (MQ=255)
                                                    tGGTACGAAAAAGACGATATGAACACCTCGGATATGc                                                  >  1:4270774/1‑37 (MQ=25)
                                                    tGGTACGAAAAAGACGATATGAACACCTCGGATATGCa                                                 >  1:705505/1‑38 (MQ=25)
                                                    tGGTACGAAAAAGACGATATGAACACCTCGGATATGCa                                                 >  1:2451133/1‑38 (MQ=25)
                                                    tGGTACGAAAAAGACGATATGAACACCTCGGATATGCa                                                 >  1:2547601/1‑38 (MQ=25)
                                                      gTACGAAAAAGACTATATGAACACCTCGGATATGCATCCGTTTATTCATCCGCTTTCTGCGGCGGTCGa                <  1:2753154/69‑1 (MQ=255)
                                                      gTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTATTCATCCGCttt                             >  1:2928721/1‑54 (MQ=255)
                                                      gTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTATTCATCCGCTTTCTGCGGCGGTCGa                <  1:774894/69‑1 (MQ=255)
                                                      gTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTATTCATCCGCTTTCTGCGGCGGTCGATc              >  1:5188932/1‑71 (MQ=255)
                                                      gTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGt                                            <  1:34185/41‑1 (MQ=255)
                                                      gTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCTGTCGAt               <  1:5336978/70‑1 (MQ=255)
                                                      gTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCGGTCGAt               <  1:2241915/70‑1 (MQ=255)
                                                      gTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCGGTCGAt               <  1:4590972/70‑1 (MQ=255)
                                                      gTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCGGTCGAt               <  1:3132333/70‑1 (MQ=255)
                                                       tACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCt                               <  1:1476946/53‑1 (MQ=255)
                                                       tACGAAAAAGACGACATAAATACTTCGGATATGCATCCGt                                            <  1:4233956/40‑1 (MQ=255)
                                                        aCGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCGGTCGATCCg            >  1:93619/1‑71 (MQ=255)
                                                         cGAAAAAGACGACATGAATACTTCGGATATGCATCCGtt                                           <  1:5180870/39‑1 (MQ=255)
                                                          gAAAAAGACGATATGAACACCTCGGATATGCATCCGtt                                           <  1:3706483/38‑1 (MQ=37)
                                                          gAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTa                                         <  1:416101/40‑1 (MQ=255)
                                                          gAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCAcc                                   <  1:533759/46‑1 (MQ=255)
                                                           aaaaaGACGACATGAATACTTCGGATATGCATCCGtt                                           >  1:59931/1‑37 (MQ=255)
                                                           aaaaaGACGACATGAATACTTCGGATATGCATCCGtt                                           >  1:2255891/1‑37 (MQ=255)
                                                           aaaaaGACGACATGAATACTTCGGATATGCATCCGTTTATTCa                                     <  1:1322700/43‑1 (MQ=255)
                                                           aaaaaGACGACATGAATACTTCGGATATGCATCCGTTTATTCa                                     <  1:1377918/43‑1 (MQ=255)
                                                           aaaaaGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCGGTCGATCCGGcc         >  1:159557/1‑71 (MQ=255)
                                                            aaaaGACGATATGAACATCTCGGATATGCATCCGTTTATTCATCCGCTTTCTGCGGCGGTCGATCCGGcgt        <  1:5196116/71‑3 (MQ=255)
                                                            aaaaGACGATATGAACACCTCGGATATGCATCCGTTTa                                         >  1:3362053/1‑38 (MQ=37)
                                                            aaaaGACGATATGAACACCTCGGATATGCATCCGTTTATTCATCCGCTTTCTGCGGCGGTCGATCCGGcgt        <  1:1165135/71‑3 (MQ=255)
                                                            aaaaGACGACATGAATACTTCGGATATGCATCCGttt                                          >  1:4894266/1‑37 (MQ=255)
                                                            aaaaGACGACATGAATACTTCGGATATGCATCCGttt                                          >  1:772551/1‑37 (MQ=255)
                                                            aaaaGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCGGTCGATCCGGcc         <  1:2971644/70‑1 (MQ=255)
                                                             aaaGACGATATGAACACCTCGGATATGCATCCGTTTATTCATCCGCTTTCTGCGGCGGTCGATCCGGCGTg       <  1:527492/71‑1 (MQ=255)
                                                                 acgacATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTgcggc                      <  1:4214709/52‑1 (MQ=255)
                                                                  cgatATGAACACCTCGGATATGCATCCGTTTATTCATCCGCttt                             >  1:2625660/1‑42 (MQ=25)
                                                                  cgatATGAACACCTCGGATATGCATCCGTTTATTCATCCGCttt                             >  1:796807/1‑42 (MQ=25)
                                                                  cgatATGAACACCTCGGATATGCATCCGTTTATTCATCCGCttt                             >  1:1265174/1‑42 (MQ=25)
                                                                   gacATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCGGTCGATCCGGCCTGGGAAg  <  1:5605469/70‑1 (MQ=255)
                                                                   gacATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCGGTCGATCCGGCCTGGGAAg  <  1:673802/70‑1 (MQ=255)
                                                                   gacATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCGGTCGATCCGGCCTGGGAAg  <  1:2757281/70‑1 (MQ=255)
                                                                    acATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCGGTCGa                <  1:295201/55‑1 (MQ=255)
                                                                     cATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTg                              >  1:4451928/1‑40 (MQ=255)
                                                                     |                                                                   
CCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCCGCTGTCTGCGGCGGTCGATCCGGCCTGGGAAG  >  minE/833864‑834000

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A