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 750,205 C→G 50.4% E1005D (GAG→GAC)  mfd ← transcription‑repair coupling factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE750,2050CG50.4% ‑1.8 / 168.0 131E1005D (GAG→GAC) mfdtranscription‑repair coupling factor
Reads supporting (aligned to +/- strand):  ref base C (35/30);  new base G (20/46);  total (55/76)
Fisher's exact test for biased strand distribution p-value = 7.98e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

Only 100 of 131 total aligned reads displayed.

TAGAACGACAGACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACGGCTCGCGTCCGGCTTTCAGTGCATC  >  minE/750140‑750270
                                                                 |                                                                 
tAGAACGACAGACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTc                                                                 <  1:2590728/68‑1 (MQ=255)
tAGAACGACAGACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTc                                                                 <  1:2234547/68‑1 (MQ=255)
tAGAACGACAGACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTc                                                                 <  1:791079/68‑1 (MQ=255)
tAGAACGACAGACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTc                                                                 <  1:2413379/68‑1 (MQ=255)
tAGAACGACAGACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTc                                                                 <  1:2417332/68‑1 (MQ=255)
 aGAACGACAGACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTc                                                                 <  1:1384036/67‑1 (MQ=255)
     cGACAGACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTc                                                           >  1:982672/1‑69 (MQ=255)
     cGACAGACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTc                                                           >  1:2741007/1‑69 (MQ=255)
     cGACAGACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTc                                                           >  1:513712/1‑69 (MQ=255)
     cGACAGACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTc                                                           >  1:584983/1‑69 (MQ=255)
       aCAGACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTg                                                         <  1:2698609/69‑1 (MQ=255)
       aCAGACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTg                                                         <  1:303836/69‑1 (MQ=255)
          gACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTc                                                                 <  1:3061557/58‑1 (MQ=255)
           aCGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATC‑‑CAGCTCGACTTCTGTTTgct                                                   <  1:2508994/69‑1 (MQ=255)
             gcgTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTgct                                                   <  1:1662138/69‑1 (MQ=255)
             gcgTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTgct                                                   <  1:3176535/69‑1 (MQ=255)
             gcgTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTgct                                                   <  1:1366393/69‑1 (MQ=255)
             gcgTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTgct                                                   <  1:3279123/69‑1 (MQ=255)
             gcgTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTgct                                                   <  1:157186/69‑1 (MQ=255)
             gcgTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTgct                                                   <  1:50811/69‑1 (MQ=255)
             gcgTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTgct                                                   <  1:1064088/69‑1 (MQ=255)
             gcgTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTgct                                                   <  1:93228/69‑1 (MQ=255)
             gcgTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTgct                                                   <  1:763806/69‑1 (MQ=255)
             gcgTGTTCACGTAAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTgct                                                   <  1:2143963/69‑1 (MQ=255)
              cgTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTgct                                                   <  1:2076621/68‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:1045289/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:2623308/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:2472612/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:2633526/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:2694329/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:2391365/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:2832267/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:3011344/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:3088282/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:3135888/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:3207447/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:3320609/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:555014/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:579484/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:713356/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:768860/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:811918/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:942214/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:239009/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:1039657/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:1205010/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:1213501/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:1443971/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:1444807/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:1486661/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:1635471/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:205227/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:2031783/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:1718818/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:1940718/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:2003380/69‑1 (MQ=255)
                            ggATGAAATCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTCCTGGCTGGTGAGATCtt                                    <  1:2211986/69‑1 (MQ=255)
                             gATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCt                                     >  1:2598440/1‑67 (MQ=255)
                             gATGAAATCATCTGGCAATAGCGACGGCATCCGAAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCt                                     >  1:1172778/1‑67 (MQ=255)
                             gATGAAATCATCTGGCAATAGCGACGGAATCCGCAGCTCGCCTTCTGTTTGCTGGCTGGTGAGATCt                                     >  1:1498929/1‑67 (MQ=255)
                              aTGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTcc                                  >  1:2083396/1‑69 (MQ=255)
                              aTGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTcc                                  >  1:853230/1‑69 (MQ=255)
                              aTGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTcc                                  >  1:3342701/1‑69 (MQ=255)
                              aTGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTcc                                  >  1:1591010/1‑69 (MQ=255)
                              aTGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTcc                                  >  1:1716101/1‑69 (MQ=255)
                                 aaaTCATCTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCtt                                    <  1:2646173/64‑1 (MQ=255)
                                 aaaTCATCTGGCAATAGCGACGGCATCCGCAGCTCg                                                                >  1:1845101/1‑36 (MQ=255)
                                 aaaTCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGc                               >  1:74838/1‑69 (MQ=255)
                                 aaaTCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGc                               >  1:2172953/1‑69 (MQ=255)
                                 aaaTCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGc                               >  1:1218256/1‑69 (MQ=255)
                                 aaaTCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGc                               >  1:1887131/1‑69 (MQ=255)
                                 aaaTCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGc                               >  1:311017/1‑69 (MQ=255)
                                 aaaTCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGc                               >  1:3187826/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACgg                          >  1:3034689/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACgg                          >  1:1184443/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACgg                          >  1:1378503/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACgg                          >  1:514691/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACgg                          >  1:2874131/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACgg                          >  1:1855570/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACgg                          >  1:446961/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACgg                          >  1:2736439/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACgg                          >  1:914899/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACgg                          >  1:1851828/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACgg                          >  1:1827801/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACgg                          >  1:3266420/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACgg                          >  1:1777392/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACgg                          >  1:3244691/1‑69 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACg                           >  1:2207221/1‑68 (MQ=255)
                                      atcTGGCAATAGCGACGGCATCCGCAGGTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACg                           >  1:221027/1‑68 (MQ=255)
                                                 gCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACGGCTCGCGTCCgg               >  1:1128449/1‑69 (MQ=255)
                                                 gCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACGGCTCGCGTCCgg               >  1:365553/1‑69 (MQ=255)
                                                 gCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACGGCTCGCGTCCgg               >  1:667973/1‑69 (MQ=255)
                                                 gCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACGGCTCGCGTCCgg               >  1:2592457/1‑69 (MQ=255)
                                                 gCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACGGCTCGCGTCCgg               >  1:3249493/1‑69 (MQ=255)
                                                            cGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACGGCTCGCGTCCGGCTTTCAGTGc     >  1:338259/1‑68 (MQ=255)
                                                            cGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACGGCTCGCGTCCGGCTTTCAGTGc     >  1:200684/1‑68 (MQ=255)
                                                              cAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACGGCTCGCGTCCGGCTTTCAGTGCATc  <  1:2431275/69‑1 (MQ=255)
                                                              cAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACGGCTCGCGTCCGGCTTTCAGTGCATc  <  1:415855/69‑1 (MQ=255)
                                                              cAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACGGCTCGCGTCCGGCTTTCAGTGCATc  <  1:86886/69‑1 (MQ=255)
                                                              cAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACGGCTCGCGTCCGGCTTTCAGTGCATc  <  1:1051780/69‑1 (MQ=255)
                                                                 |                                                                 
TAGAACGACAGACGCGTGTTCACGTCAGGGATGAAATCATCTGGCAATAGCGACGGCATCCGCAGCTCGACTTCTGTTTGCTGGCTGGTGAGATCTTCCAGCGACGGCTCGCGTCCGGCTTTCAGTGCATC  >  minE/750140‑750270

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