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 1,505,057 C→T 65.4% A70A (GCC→GCT)  yfbR → deoxyribonucleoside 5'‑monophosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,505,0570CT65.4% 91.3 / 77.0 130A70A (GCC→GCT) yfbRdeoxyribonucleoside 5'‑monophosphatase
Reads supporting (aligned to +/- strand):  ref base C (29/16);  new base T (37/48);  total (66/64)
Fisher's exact test for biased strand distribution p-value = 2.76e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01

Only 100 of 130 total aligned reads displayed.

AATCGAAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTCCCTACTCCGGTGAAATACTTCAATTCGCAAATCGCTCAGG  >  minE/1504992‑1505121
                                                                 |                                                                
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:1205227/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:1601919/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:373673/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:51333/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:1700027/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:766900/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:3423915/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:1287381/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:1950620/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:1993614/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:3323342/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:2118655/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:2329629/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:254022/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:2659101/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:3125251/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:2905891/69‑1 (MQ=255)
aaTCGTAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:985727/69‑1 (MQ=255)
  tCGAAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGa                                                             <  1:3364714/69‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:1558986/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:2540480/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:260578/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:2676929/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:890321/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:2736884/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:3175810/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:1983318/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:2792426/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:28047/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:97457/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:1800303/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:1341183/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:1713004/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:1030351/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:2999766/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:1622242/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:1587534/68‑1 (MQ=255)
         tttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTAAGAAGTGCt                                                       <  1:2958209/68‑1 (MQ=255)
         tttGGAGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:3319895/68‑1 (MQ=255)
          ttGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCt                                                       <  1:1881151/67‑1 (MQ=255)
                  aaTGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGAt                                             >  1:3090382/1‑69 (MQ=255)
                     gTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGAtctc                                          >  1:3062053/1‑69 (MQ=255)
                     gTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGAtctc                                          >  1:3084697/1‑69 (MQ=255)
                     gTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGAtctc                                          >  1:1119792/1‑69 (MQ=255)
                     gTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGAtctc                                          >  1:2389947/1‑69 (MQ=255)
                     gTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGAtctc                                          >  1:1514906/1‑69 (MQ=255)
                     gTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGAtctc                                          >  1:1258447/1‑69 (MQ=255)
                     gTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGAtctc                                          >  1:1980596/1‑69 (MQ=255)
                     gTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTACTCACCGGCGAtct                                           >  1:509403/1‑68 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATTCCTCAGAAGTGCTCACCGGCGATCTccc                                        <  1:3056226/68‑1 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATTCCTCAGAAGTGCTCACCGGCGATCTccc                                        <  1:2646631/68‑1 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCa                                                               <  1:2721662/45‑1 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTccc                                        <  1:2281166/68‑1 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTccc                                        <  1:2215688/68‑1 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTccc                                        <  1:2612601/68‑1 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTccc                                        <  1:2978564/68‑1 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTccc                                        <  1:1172472/68‑1 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTccc                                        <  1:2922496/68‑1 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTccc                                        <  1:873964/68‑1 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTccc                                        <  1:1488782/68‑1 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTcc                                         >  1:1121182/1‑67 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTCCCt                                       >  1:2422486/1‑69 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTCCCt                                       >  1:1023428/1‑69 (MQ=255)
                        aaCGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTCCCt                                       >  1:1909771/1‑69 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTTCCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:3205371/1‑55 (MQ=39)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCa                                                     >  1:2443928/1‑53 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:566439/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:3235429/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:2497204/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:390158/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:957447/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:492349/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:3263989/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:3317778/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:2118235/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:1376531/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:1540460/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:1635946/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:166972/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:1679839/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:1717896/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:1258189/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:1188793/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:2149379/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:1074383/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:2258728/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:2269202/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:2540936/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:2751762/1‑55 (MQ=255)
                          cGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAc                                                    >  1:2447798/1‑54 (MQ=255)
                          cGCCGAACGTATCGCTCTACTGGCGATGTACCACGATGCTTCAGAAGTGCTCAcc                                                   >  1:433825/1‑55 (MQ=39)
                                    aTCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTCCCTACTCCGGTGaaa                           <  1:1036573/69‑1 (MQ=255)
                                     tCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTCCCTACTCCGGTGAAAt                          >  1:2884467/1‑69 (MQ=255)
                                     tCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTCCCTACTCCGGTGAAAt                          >  1:1378737/1‑69 (MQ=255)
                                     tCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTCCCTACTCCGGTGAAAt                          >  1:1439397/1‑69 (MQ=255)
                                     tCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTCCCTACTCCGGTGAAAt                          >  1:2115821/1‑69 (MQ=255)
                                                      tACCACGATGCCTCAGAAGTGCTCACCGGCGATCTCCCTACTCCGGTGAAATACTTCAATTCGCAAATc         >  1:3319881/1‑69 (MQ=255)
                                                      tACCACGATGCCTCAGAAGTGCTCACCGGCGATCTCCCTACTCCGGTGAAATACTTCAATTCGCAAATc         >  1:2887242/1‑69 (MQ=255)
                                                      tACCACGATGCCTCAGAAGTGCTCACCGGCGATCTCCCTACTCCGGTGAAATACTTCAATTCGCAAATc         >  1:1024582/1‑69 (MQ=255)
                                                              tGCCTCAGAAGTGCTCACCGGCGATCTCCCTACTCCGGTGAAATACTTCAATTCGCAAATCGCTCAgg  >  1:3418334/1‑68 (MQ=255)
                                                                 |                                                                
AATCGAAAATTTGGCGGTAATGTCAACGCCGAACGTATCGCTTTACTGGCGATGTACCACGATGCCTCAGAAGTGCTCACCGGCGATCTCCCTACTCCGGTGAAATACTTCAATTCGCAAATCGCTCAGG  >  minE/1504992‑1505121

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A