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 835,160 A→C 24.1% A1206A (GCA→GCC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,1600AC24.1% 150.3 / 72.3 108A1206A (GCA→GCC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base A (36/46);  new base C (16/10);  total (52/56)
Fisher's exact test for biased strand distribution p-value = 1.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

Only 100 of 113 total aligned reads displayed.

GTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAG  >  minE/835090‑835229
                                                                      |                                                                     
gtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCa                                                                       >  1:325779/1‑71 (MQ=255)
gtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCa                                                                       >  1:2730619/1‑71 (MQ=255)
gtATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCa                                                                       <  1:3411705/71‑1 (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)
                   ccGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATg                                                    >  1:636062/1‑71 (MQ=255)
                   ccGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATg                                                    >  1:2121472/1‑71 (MQ=255)
                   cagTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAActacta                                                      >  1:629274/3‑69 (MQ=255)
                     gTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGc                                                  <  1:4671923/71‑1 (MQ=255)
                        tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCGATCTGGCATACGGCTTTAACTACTATGGCAcc                                               >  1:2397428/1‑71 (MQ=255)
                        tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCAcc                                               >  1:5184292/1‑71 (MQ=255)
                        tCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCAcc                                               >  1:916686/1‑71 (MQ=255)
                          tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                                             >  1:1028244/4‑71 (MQ=255)
                          tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                                             >  1:3265087/4‑71 (MQ=255)
                          tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                                             >  1:1140659/4‑71 (MQ=255)
                          tgcccGAAACCAACGCATATGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGt                                             >  1:757117/4‑71 (MQ=255)
                          aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAActacta                                                      >  1:2769493/1‑62 (MQ=255)
                          aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                              >  1:5120562/1‑70 (MQ=255)
                          aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                              <  1:659377/70‑1 (MQ=255)
                          aCGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                              <  1:3495520/70‑1 (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                                             <  1:4346845/68‑1 (MQ=255)
                             ccGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGt                                             <  1:2645374/68‑1 (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                                        >  1:1801658/1‑69 (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                             <  1:1623867/71‑1 (MQ=255)
                                          atatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGAt                             <  1:3939814/71‑1 (MQ=255)
                                           tatGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCGCCGtcg                                           <  1:1800593/56‑3 (MQ=255)
                                           tatGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGtcg                                           >  1:4731269/1‑54 (MQ=255)
                                           tatGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                                              <  1:737849/37‑1 (MQ=255)
                                           tatGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                                              <  1:3473633/37‑1 (MQ=255)
                                           tatGATCGGCGGCTATGCCCATCTGGCATACGGCttt                                                              <  1:4150475/37‑1 (MQ=255)
                                           tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                      <  1:2636473/61‑1 (MQ=255)
                                           tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                      <  1:1760513/61‑1 (MQ=255)
                                           tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATg                            <  1:387810/71‑1 (MQ=255)
                                           tatGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATg                            <  1:5284471/71‑1 (MQ=255)
                                             tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGAt                             >  1:480016/1‑68 (MQ=255)
                                             tGATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATg                            <  1:1093244/69‑1 (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)
                                             tGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAg                          <  1:5188796/71‑1 (MQ=255)
                                              gATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGt                         >  1:805842/1‑71 (MQ=255)
                                              gATTGGCGGTTACGCGCAGCTGGCCTGGGGCTTTAACTACTACGGCACCGTCGGATCGAACCGCGATGAGt                         >  1:1260521/1‑71 (MQ=255)
                                              gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                              >  1:3029433/1‑50 (MQ=255)
                                              gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                              >  1:2545977/1‑50 (MQ=255)
                                              gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCg                                              >  1:3139929/1‑50 (MQ=255)
                                              gATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGt                         >  1:2967366/1‑71 (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)
                                                       cTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTa                 >  1:3173179/1‑70 (MQ=255)
                                                       cTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACAGCGATGAGttt                       >  1:4370012/1‑64 (MQ=255)
                                                        tATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGt               >  1:235901/1‑71 (MQ=255)
                                                         aTGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTATGTTCTAACcgcg                               <  1:3713206/54‑1 (MQ=255)
                                                          tGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTttg                      <  1:4504329/62‑1 (MQ=255)
                                                            cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                      <  1:2125127/44‑1 (MQ=255)
                                                            cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCt                                      <  1:4788922/44‑1 (MQ=255)
                                                            cccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTaa                                    >  1:725216/1‑46 (MQ=255)
                                                             ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAg                >  1:4510044/1‑65 (MQ=255)
                                                             ccATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAg                >  1:4361515/1‑65 (MQ=255)
                                                                     cATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaag  <  1:3865259/71‑1 (MQ=255)
                                                                     cATACGGCTTTAACTACTATGGCACCGTAGGTCCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATgaag  <  1:3211259/71‑1 (MQ=255)
                                                                      |                                                                     
GTATCCATAACTCGGTCACCCGTATCACGCCGAAACCGACGCATATGATCGGCGGCTATGCCCATCTGGCATACGGCTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAG  >  minE/835090‑835229

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