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 835,145 C→T 22.8% G1201G (GGC→GGT)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,1450CT22.8% 195.5 / 52.1 105G1201G (GGC→GGT) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (35/46);  new base T (16/8);  total (51/54)
Fisher's exact test for biased strand distribution p-value = 6.22e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 113 total aligned reads displayed.

CAGCGTGGTGGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTA  >  minE/835080‑835214
                                                                 |                                                                     
    gtggtgGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCAt                                                              <  1:3274302/71‑1 (MQ=255)
    gtggtgGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCAt                                                              <  1:3347137/71‑1 (MQ=255)
    gtggtgGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCAt                                                              <  1:3182946/71‑1 (MQ=255)
      ggtggtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCt                                                            >  1:5078199/1‑71 (MQ=255)
      ggtggtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCt                                                            >  1:1600360/1‑71 (MQ=255)
          gtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGc                                                         >  1:5168995/1‑70 (MQ=255)
          gtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCa                                                        >  1:325779/1‑71 (MQ=255)
          gtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCa                                                        >  1:2730619/1‑71 (MQ=255)
               cATAACTCGGTTACCCGCGTTTGCCCGAAACCAACGCATATGATTGGCGGTTacg                                                                   >  1:1532665/1‑53 (MQ=255)
               cATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACgg                                                   >  1:4713592/1‑71 (MQ=255)
               cATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACg                                                    <  1:33495/70‑1 (MQ=255)
                aTAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGc                                                  >  1:1804288/1‑71 (MQ=255)
                   aCTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCa                                                        <  1:2132096/62‑1 (MQ=255)
                   aCTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                               <  1:5049240/71‑1 (MQ=255)
                   aCTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCtt                                                <  1:4279327/70‑1 (MQ=255)
                   aCTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCt                                                 >  1:1977432/1‑69 (MQ=255)
                   aCTCGGTCACCCGTATCACGCAGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                               <  1:1174669/71‑1 (MQ=255)
                     tCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGCCTATGCCCATCTGGCATACGGCttt                                               <  1:1404137/69‑1 (MQ=255)
                      cGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAac                                            >  1:5690437/1‑71 (MQ=255)
                        gTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCa                                                        <  1:3962265/57‑1 (MQ=255)
                           aCCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAActacta                                       >  1:4035309/1‑71 (MQ=255)
                             ccGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGccc                                                                <  1:3776229/44‑1 (MQ=255)
                             ccGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATg                                     >  1:636062/1‑71 (MQ=255)
                             cagTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAActacta                                       >  1:629274/3‑69 (MQ=255)
                               gTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGc                                   <  1:3519468/71‑1 (MQ=255)
                               gTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGc                                   <  1:4671923/71‑1 (MQ=255)
                                 aTCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCAt                                                              >  1:2578909/1‑42 (MQ=255)
                                  tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCGATCTGGCATACGGCTTTAACTACTATGGCAcc                                >  1:2397428/1‑71 (MQ=255)
                                  tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTgg                                                          <  1:874635/45‑1 (MQ=255)
                                  tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTgg                                                          <  1:4887088/45‑1 (MQ=255)
                                  tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTgg                                                          <  1:1957910/45‑1 (MQ=255)
                                  tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCAcc                                >  1:916686/1‑71 (MQ=255)
                                  tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCAcc                                >  1:5184292/1‑71 (MQ=255)
                                    tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                              >  1:1140659/4‑71 (MQ=255)
                                    tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                              >  1:3265087/4‑71 (MQ=255)
                                    tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                              >  1:1028244/4‑71 (MQ=255)
                                    tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                              >  1:757117/4‑71 (MQ=255)
                                    aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                               >  1:261888/1‑70 (MQ=255)
                                    aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                               <  1:4760013/70‑1 (MQ=255)
                                    aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                               <  1:3495520/70‑1 (MQ=255)
                                    aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                               >  1:5120562/1‑70 (MQ=255)
                                    aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                               <  1:659377/70‑1 (MQ=255)
                                    aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                              <  1:263755/71‑1 (MQ=255)
                                     gcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGtc                             >  1:1715357/3‑70 (MQ=255)
                                      gCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAg                            <  1:829241/71‑1 (MQ=255)
                                       ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                              <  1:2645374/68‑1 (MQ=255)
                                       ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                              <  1:4346845/68‑1 (MQ=255)
                                       ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                              <  1:356987/68‑1 (MQ=255)
                                        cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                          >  1:188003/1‑71 (MQ=255)
                                         gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                               <  1:4849503/49‑1 (MQ=255)
                                         gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAg                            >  1:1201454/1‑68 (MQ=255)
                                         gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                         >  1:936588/1‑71 (MQ=255)
                                         gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                         <  1:2364718/71‑1 (MQ=255)
                                         gAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCggat                         >  1:1957960/1‑69 (MQ=255)
                                          aaaCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTc                        >  1:1058404/1‑71 (MQ=255)
                                           aaCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTaa                                             >  1:462480/1‑49 (MQ=255)
                                           aaCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                       <  1:5628827/71‑1 (MQ=255)
                                           aaCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATcg                       <  1:2752210/71‑2 (MQ=255)
                                           aaCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATc                        >  1:2485470/1‑70 (MQ=255)
                                            aCCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                               <  1:4869451/46‑1 (MQ=255)
                                            aCCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATcga                      <  1:1155060/71‑3 (MQ=255)
                                             ccaaCGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGaa                     <  1:2363058/68‑1 (MQ=255)
                                             ccGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTaa                     <  1:3133452/71‑1 (MQ=255)
                                               gACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                               <  1:3878354/43‑1 (MQ=255)
                                                aCGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACcg                  >  1:194914/1‑71 (MQ=255)
                                                 cGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc                 <  1:3139153/71‑1 (MQ=255)
                                                 cGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc                 <  1:5627680/71‑1 (MQ=255)
                                                  gCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc                 >  1:1627846/1‑70 (MQ=255)
                                                    atatGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGAt              <  1:2074863/71‑1 (MQ=255)
                                                    atatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt              <  1:3939814/71‑1 (MQ=255)
                                                    atatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt              <  1:1623867/71‑1 (MQ=255)
                                                     tatGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCGCCGtcg                            <  1:1800593/56‑3 (MQ=255)
                                                     tatGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGtcg                            >  1:4731269/1‑54 (MQ=255)
                                                     tatGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                               <  1:3473633/37‑1 (MQ=255)
                                                     tatGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                               <  1:4150475/37‑1 (MQ=255)
                                                     tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                       <  1:1760513/61‑1 (MQ=255)
                                                     tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                       <  1:2636473/61‑1 (MQ=255)
                                                     tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATg             <  1:5284471/71‑1 (MQ=255)
                                                     tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATg             <  1:387810/71‑1 (MQ=255)
                                                      atGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                       <  1:3015777/60‑1 (MQ=255)
                                                       tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATg             <  1:1835323/69‑1 (MQ=255)
                                                       tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATg             <  1:1093244/69‑1 (MQ=255)
                                                       tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGa            >  1:3248356/1‑70 (MQ=255)
                                                       tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGa            <  1:3098752/70‑1 (MQ=255)
                                                       tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAg           >  1:4471661/1‑71 (MQ=255)
                                                       tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTaa                                             >  1:4231638/1‑37 (MQ=255)
                                                       tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTaa                                             >  1:5210063/1‑37 (MQ=255)
                                                        gATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGt          >  1:805842/1‑71 (MQ=255)
                                                        gATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGt          >  1:1260521/1‑71 (MQ=255)
                                                        gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                               >  1:2545977/1‑50 (MQ=255)
                                                        gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                               >  1:2255828/1‑50 (MQ=255)
                                                        gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                               >  1:3029433/1‑50 (MQ=255)
                                                        gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                               >  1:3139929/1‑50 (MQ=255)
                                                        gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGt          >  1:2967366/1‑71 (MQ=255)
                                                          ttggcggtTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGttc        <  1:4466787/69‑2 (MQ=255)
                                                          ttggcggtTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGttc        <  1:3090538/69‑2 (MQ=255)
                                                           tggcggtTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGttca       >  1:4320174/2‑69 (MQ=255)
                                                             gcggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                              <  1:2652078/46‑1 (MQ=255)
                                                              cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg    <  1:809850/71‑1 (MQ=255)
                                                              cggcTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttgttg    <  1:3619986/71‑1 (MQ=255)
                                                                 |                                                                     
CAGCGTGGTGGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTA  >  minE/835080‑835214

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A