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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,584,700 T→G 35.9% T60T (ACT→ACG)  cysZ → predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,584,7000TG35.9% 58.2 / 79.4 92T60T (ACT→ACG) cysZpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (37/22);  new base G (28/5);  total (65/27)
Fisher's exact test for biased strand distribution p-value = 3.20e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.96e-01

TTTTGTTGATGGGGGGCGCATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCATC  >  minE/1584639‑1584766
                                                             |                                                                  
ttttGTTGATGGGGGGCGCATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGa                                                             >  1:3368169/1‑69 (MQ=255)
ttttGTTGATGGGGGGCGCATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGa                                                             >  1:1656710/1‑69 (MQ=255)
    gttgATGGGGGGCGCATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGtt                                                          <  1:3393248/68‑1 (MQ=255)
    gttgATGGGGGGCGCATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGtt                                                          <  1:3233477/68‑1 (MQ=255)
    gttgATGGGGGGCGCATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGtt                                                          <  1:1501015/68‑1 (MQ=255)
    gttgATGGGGGGCGCATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGtt                                                          <  1:2109739/68‑1 (MQ=255)
    gttgATGGGGGGCGCATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGtt                                                          <  1:1540765/68‑1 (MQ=255)
                  cATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTgg                                            >  1:1351790/1‑68 (MQ=255)
                  cATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGc                                           >  1:99375/1‑69 (MQ=255)
                  cATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGc                                           >  1:3102091/1‑69 (MQ=255)
                  cATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGc                                           >  1:3083086/1‑69 (MQ=255)
                  cATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGc                                           >  1:2791060/1‑69 (MQ=255)
                  cATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGc                                           >  1:2633070/1‑69 (MQ=255)
                  cATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGc                                           >  1:2467445/1‑69 (MQ=255)
                  cATTCTGGTGGCTCTTTACACAGCTCGATGTCAGGATCACGACTCTCAtca                                                             >  1:2568951/1‑49 (MQ=255)
                     tCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTAc                                        <  1:1347821/69‑1 (MQ=255)
                      cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                       >  1:1098697/1‑69 (MQ=255)
                      cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                       >  1:2608994/1‑69 (MQ=255)
                      cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                       >  1:2653982/1‑69 (MQ=255)
                      cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                       >  1:2465096/1‑69 (MQ=255)
                      cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                       >  1:2349106/1‑69 (MQ=255)
                      cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                       >  1:276991/1‑69 (MQ=255)
                      cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                       >  1:2155589/1‑69 (MQ=255)
                      cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                       >  1:2060367/1‑69 (MQ=255)
                      cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                       >  1:569570/1‑69 (MQ=255)
                      cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                       >  1:3011016/1‑69 (MQ=255)
                      cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                       >  1:1258968/1‑69 (MQ=255)
                      cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                       >  1:681218/1‑69 (MQ=255)
                      cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                       >  1:3200632/1‑69 (MQ=255)
                      cTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACa                                       >  1:3250385/1‑69 (MQ=255)
                         gtggCTCTTTACACAGCTCGATGTCTGGATCCCGActct                                                                  <  1:485144/39‑1 (MQ=255)
                            gCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATgg                                   >  1:2500654/1‑67 (MQ=255)
                            gCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATgg                                   >  1:2868340/1‑67 (MQ=255)
                            gCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATgg                                   >  1:500619/1‑67 (MQ=255)
                            gCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATgg                                   >  1:3260482/1‑67 (MQ=255)
                            gCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATgg                                   >  1:1060213/1‑67 (MQ=255)
                               ctTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGa                               >  1:1054691/1‑68 (MQ=255)
                               ctTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGa                               >  1:2495943/1‑68 (MQ=255)
                                  tACGCAACTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCg                                                  >  1:2597800/1‑46 (MQ=255)
                                  tACGCAACTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCg                                                  >  1:457661/1‑46 (MQ=255)
                                  tACGCAACTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCg                                                  >  1:716150/1‑46 (MQ=255)
                                  tACGCAACTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCg                                                  >  1:691506/1‑46 (MQ=255)
                                  tACGCAACTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCg                                                  >  1:1337959/1‑46 (MQ=255)
                                  tACGCAACTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCg                                                  >  1:22791/1‑46 (MQ=255)
                                  tACGCAACTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCg                                                  >  1:3275540/1‑46 (MQ=255)
                                  tACGCAACTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCg                                                  >  1:2042073/1‑46 (MQ=255)
                                  tACGCAACTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCg                                                  >  1:1970666/1‑46 (MQ=255)
                                  tACGCAACTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCg                                                  >  1:606970/1‑46 (MQ=255)
                                        acTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCtgtt                     <  1:2475477/68‑1 (MQ=255)
                                        acTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCtgtt                     <  1:2552903/68‑1 (MQ=255)
                                        acTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCtgtt                     <  1:1645628/68‑1 (MQ=255)
                                         cTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCtgtt                     <  1:476562/68‑1 (MQ=255)
                                         cTCGATGTCTGGATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCtgtt                     <  1:1631636/68‑1 (MQ=255)
                                              tGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGc                <  1:2876874/68‑1 (MQ=255)
                                              tGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGc                <  1:2895446/68‑1 (MQ=255)
                                              tGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGc                <  1:3013761/68‑1 (MQ=255)
                                                  tGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTg           >  1:2313864/1‑69 (MQ=255)
                                                  tGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTg           >  1:2309420/1‑69 (MQ=255)
                                                  tGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTg           >  1:3186400/1‑69 (MQ=255)
                                                  tGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTg           >  1:1512148/1‑69 (MQ=255)
                                                  tGGATCCCGACTCACATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCctct            >  1:1599402/1‑68 (MQ=255)
                                                    taTCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:1823269/2‑69 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCtgt                      >  1:2885525/1‑56 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTgg          >  1:1656231/1‑68 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTgg          >  1:1405565/1‑68 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:584755/1‑69 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:3261801/1‑69 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:509850/1‑69 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:1030209/1‑69 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:1903735/1‑69 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:1912344/1‑69 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:2130018/1‑69 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:3093523/1‑69 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:2936995/1‑69 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:2931278/1‑69 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:1645437/1‑69 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:1029222/1‑69 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:1527644/1‑69 (MQ=255)
                                                    gATCCCGACGCTCATGAGTTATGTTCCGGACTGGTTACAATGGCTGAGCTATCTGTTGTGGCCCCTGGc         >  1:2290194/1‑69 (MQ=255)
                                                       cccGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGt      >  1:1875702/1‑69 (MQ=255)
                                                          gACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt   <  1:2513585/69‑1 (MQ=255)
                                                          gACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt   <  1:2332980/69‑1 (MQ=255)
                                                          gACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt   <  1:409736/69‑1 (MQ=255)
                                                          gACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt   <  1:3258972/69‑1 (MQ=255)
                                                          gACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt   <  1:793840/69‑1 (MQ=255)
                                                          gACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt   <  1:867232/69‑1 (MQ=255)
                                                           aCTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAtc  <  1:1731478/69‑1 (MQ=255)
                                                           aCTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAtc  <  1:3245384/69‑1 (MQ=255)
                                                           aCTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAtc  <  1:2472598/69‑1 (MQ=255)
                                                           aCTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAtc  <  1:3400058/69‑1 (MQ=255)
                                                           aCTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAtc  <  1:2721406/69‑1 (MQ=255)
                                                           aCTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAtc  <  1:1180467/69‑1 (MQ=255)
                                                           aCTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt   <  1:3216630/68‑1 (MQ=255)
                                                             tctcATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCAt   <  1:1630439/66‑1 (MQ=255)
                                                             |                                                                  
TTTTGTTGATGGGGGGCGCATTCTGGTGGCTCTTTACACAGCTCGATGTCTGGATCCCGACTCTCATGAGTTACGTTCCGGACTGGCTACAATGGCTGAGTTATCTGTTGTGGCCTCTGGCTGTCATC  >  minE/1584639‑1584766

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