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 835,139 C→T 22.8% I1199I (ATC→ATT)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,1390CT22.8% 193.7 / 53.2 105I1199I (ATC→ATT) 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 = 6.57e-01

Only 100 of 120 total aligned reads displayed.

AAATTACCCAACAGCGTGGTGGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGT  >  minE/835069‑835206
                                                                      |                                                                   
aaaTTACCCAACAGCGTGGTGGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATc                                                                     <  1:750730/71‑1 (MQ=255)
aaaTTACCCAACAGCGTGGTGGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATc                                                                     <  1:2220741/71‑1 (MQ=255)
 aaTTACCCAACAGCGTGGTGGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATcg                                                                    >  1:1784043/1‑71 (MQ=255)
 aaTTACCCAACAGCGTGGTGGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATcg                                                                    >  1:123202/1‑71 (MQ=255)
 aaTTACCCAACAGCGTGGTGGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGAATATGATcg                                                                    >  1:1512066/1‑71 (MQ=255)
   ttACCCAACAGCGTGGTGGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATcggc                                                                  >  1:4522238/1‑71 (MQ=255)
     aCCCAACAGCGTGGTGGTATCCATAACTCGGTCACCAGTATCACGCCGAAACCGACGCATATGATcggcgg                                                                >  1:2328573/1‑71 (MQ=255)
           cAGCGTGGTGGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGc                                                          >  1:1272962/1‑71 (MQ=255)
               gtggtgGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCAt                                                      <  1:3347137/71‑1 (MQ=255)
               gtggtgGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCAt                                                      <  1:3274302/71‑1 (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                                                <  1:3411705/71‑1 (MQ=255)
                     gtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCa                                                >  1:325779/1‑71 (MQ=255)
                     gtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCa                                                >  1:2730619/1‑71 (MQ=255)
                        ttcATAACTCGGTTACCCGCGTTTGCCCGAAACCAACGCATATGATtggc                                                                  <  1:963006/48‑1 (MQ=255)
                         ccATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATcgg                                                                   <  1:2541232/48‑1 (MQ=255)
                         ccATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATcgg                                                                   <  1:1839152/48‑1 (MQ=255)
                          cATAACTCGGTTACCCGCGTTTGCCCGAAACCAACGCATATGATTGGCGGTTacg                                                           >  1:1532665/1‑53 (MQ=255)
                          cATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACg                                            <  1:33495/70‑1 (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)
                                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                                                        <  1:3886358/44‑1 (MQ=255)
                                        ccGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGccc                                                        <  1:3776229/44‑1 (MQ=255)
                                        ccGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATg                             >  1:2121472/1‑71 (MQ=255)
                                        ccGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATg                             >  1:636062/1‑71 (MQ=255)
                                          gTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGc                           <  1:4671923/71‑1 (MQ=255)
                                            aTCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCAt                                                      >  1:2578909/1‑42 (MQ=255)
                                             tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCGATCTGGCATACGGCTTTAACTACTATGGCAcc                        >  1:2397428/1‑71 (MQ=255)
                                             tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTgg                                                  <  1:1957910/45‑1 (MQ=255)
                                             tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTgg                                                  <  1:874635/45‑1 (MQ=255)
                                             tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCAcc                        >  1:5184292/1‑71 (MQ=255)
                                             tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCAcc                        >  1:916686/1‑71 (MQ=255)
                                               tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                      >  1:1140659/4‑71 (MQ=255)
                                               tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                      >  1:757117/4‑71 (MQ=255)
                                               tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                      >  1:3265087/4‑71 (MQ=255)
                                               tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                      >  1:1028244/4‑71 (MQ=255)
                                               aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAActacta                               >  1:2769493/1‑62 (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)
                                               aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                       >  1:261888/1‑70 (MQ=255)
                                               aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                      <  1:263755/71‑1 (MQ=255)
                                                gcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGtc                     >  1:1715357/3‑70 (MQ=255)
                                                 gCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                       <  1:2557802/52‑1 (MQ=255)
                                                 gCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAg                    <  1:829241/71‑1 (MQ=255)
                                                  ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                      <  1:356987/68‑1 (MQ=255)
                                                  ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                      <  1:4346845/68‑1 (MQ=255)
                                                  ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                      <  1:2645374/68‑1 (MQ=255)
                                                   cGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGt                  >  1:188003/1‑71 (MQ=255)
                                                    gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                       <  1:4849503/49‑1 (MQ=255)
                                                    gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAg                    >  1:1201454/1‑68 (MQ=255)
                                                    gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                 <  1:2364718/71‑1 (MQ=255)
                                                    gAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGtt                 >  1:936588/1‑71 (MQ=255)
                                                    gAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCggat                 >  1:1801658/1‑69 (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)
                                                       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         <  1:5627680/71‑1 (MQ=255)
                                                            cGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc         <  1:3139153/71‑1 (MQ=255)
                                                             gCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACcgc         >  1:1627846/1‑70 (MQ=255)
                                                               atatGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGAt      <  1:2074863/71‑1 (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                                       <  1:737849/37‑1 (MQ=255)
                                                                tatGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                       <  1:4150475/37‑1 (MQ=255)
                                                                tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt               <  1:1760513/61‑1 (MQ=255)
                                                                tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATg     <  1:387810/71‑1 (MQ=255)
                                                                tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATg     <  1:5284471/71‑1 (MQ=255)
                                                                 atGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt               <  1:3015777/60‑1 (MQ=255)
                                                                  tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGAt      >  1:480016/1‑68 (MQ=255)
                                                                  tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATg     <  1:1093244/69‑1 (MQ=255)
                                                                  tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATg     <  1:1835323/69‑1 (MQ=255)
                                                                  tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGa    <  1:3098752/70‑1 (MQ=255)
                                                                  tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGa    >  1:3248356/1‑70 (MQ=255)
                                                                  tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAg   >  1:4471661/1‑71 (MQ=255)
                                                                  tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTaa                                     >  1:4231638/1‑37 (MQ=255)
                                                                  tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTaa                                     >  1:5210063/1‑37 (MQ=255)
                                                                   gATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGt  >  1:1260521/1‑71 (MQ=255)
                                                                   gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                       >  1:2255828/1‑50 (MQ=255)
                                                                   gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                       >  1:2545977/1‑50 (MQ=255)
                                                                   gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                       >  1:3029433/1‑50 (MQ=255)
                                                                      |                                                                   
AAATTACCCAACAGCGTGGTGGTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGT  >  minE/835069‑835206

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