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 1,976,156 C→A 63.9% T293T (ACC→ACA)  galP → D‑galactose transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,976,1560CA63.9% 78.6 / 101.6 119T293T (ACC→ACA) galPD‑galactose transporter
Reads supporting (aligned to +/- strand):  ref base C (29/14);  new base A (31/45);  total (60/59)
Fisher's exact test for biased strand distribution p-value = 7.34e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

Only 100 of 119 total aligned reads displayed.

GTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTATCGCAATCGGCCTTGTTGACCGCTGGG  >  minE/1976090‑1976220
                                                                  |                                                                
gTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGt                                                                >  1:594349/1‑69 (MQ=255)
gTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGt                                                                >  1:3266538/1‑69 (MQ=255)
 tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                                               >  1:3022339/1‑69 (MQ=255)
 tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                                               >  1:503658/1‑69 (MQ=255)
 tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                                               >  1:364434/1‑69 (MQ=255)
 tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                                               >  1:2379822/1‑69 (MQ=255)
 tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                                               >  1:1517290/1‑69 (MQ=255)
 tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                                               >  1:1224801/1‑69 (MQ=255)
 tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                                               >  1:2796180/1‑69 (MQ=255)
 tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                                               >  1:1140046/1‑69 (MQ=255)
            gAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCt                                                    <  1:1048007/69‑1 (MQ=255)
            gAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCt                                                    <  1:580213/69‑1 (MQ=255)
            gAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCt                                                    <  1:2072048/69‑1 (MQ=255)
            gAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCt                                                    <  1:691002/69‑1 (MQ=255)
            gAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCt                                                    <  1:1348755/69‑1 (MQ=255)
             aaaaTCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCt                                                    <  1:146330/68‑1 (MQ=255)
                       aaCTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGGCGGCCTGACCAACGTa                                          <  1:2396679/68‑1 (MQ=255)
                         cTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACtt                                       >  1:2749044/1‑69 (MQ=255)
                           ggCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACtttc                                     >  1:3241652/1‑67 (MQ=255)
                           ggCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTg                                      >  1:854269/1‑68 (MQ=255)
                           ggCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGc                                     >  1:729451/1‑69 (MQ=255)
                           ggCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGc                                     >  1:3409584/1‑69 (MQ=255)
                           ggCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGc                                     >  1:1832693/1‑69 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTTATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:473523/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:2013091/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:897596/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:457907/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:440510/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:2257278/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:3195586/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:2508263/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:2687606/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:684869/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:1372053/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:768696/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:1464188/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:1537254/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:1910292/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:857864/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:171405/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:1065849/69‑1 (MQ=255)
                                  tataCCAACACCACCGAGCAAATGTGGCGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              <  1:2188551/69‑1 (MQ=255)
                                   ataCCAACACCACCGGGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:2610449/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCt                                                    >  1:2154000/1‑46 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              >  1:1704580/1‑68 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              >  1:3233538/1‑68 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              >  1:1870238/1‑68 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:334242/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:850113/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:885559/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:2503597/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:3234363/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:759911/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:710143/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:35078/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:69375/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:553455/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:547653/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:534839/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:2011156/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:1027870/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:1054258/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:1172641/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:1202211/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:1381909/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:1403645/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:159633/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:1598879/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:1649091/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:1800198/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:1883092/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:2888683/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:2026236/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:2094825/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:2103735/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:2311084/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:2330469/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:2346434/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:2862813/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:269315/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:2525806/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:2497375/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             >  1:2415383/1‑69 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACAAACGTACTTGCCACCttt                              >  1:3013614/1‑68 (MQ=255)
                                   ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCAGCCTGACCAACGTACTTGCCACCTTTa                             <  1:2902040/69‑1 (MQ=255)
                                   ataCCAACACCACCGAGAAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt                              >  1:151378/1‑68 (MQ=255)
                                        aaCACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTATCGc                         <  1:439877/68‑1 (MQ=255)
                                         acacTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGAcc                                                >  1:70491/1‑44 (MQ=255)
                                         acacTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGAc                                                 >  1:733063/1‑43 (MQ=255)
                                              aCCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCa                                               >  1:2367261/1‑40 (MQ=255)
                                              aCCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTATCGCAATCgg                   >  1:1857081/1‑68 (MQ=255)
                                              aCCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTATCGCAATCGGc                  >  1:1003523/1‑69 (MQ=255)
                                              aCCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTATCGCAATCGGc                  >  1:1541309/1‑69 (MQ=255)
                                                 gAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTATCGCAATCGGCCtt               <  1:1718570/69‑1 (MQ=255)
                                                 gAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTATCGCAATCGGCCtt               <  1:3332378/69‑1 (MQ=255)
                                                 gAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:1331563/55‑1 (MQ=255)
                                                         gtgGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa                             <  1:652729/47‑1 (MQ=255)
                                                              ggACCGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTATCGCAATCGGCCTTGTTGACCGCTggg  <  1:1738415/69‑1 (MQ=255)
                                                              ggACCGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTATCGCAATCGGCCTTGTTGACCGCTggg  <  1:428247/69‑1 (MQ=255)
                                                              ggACCGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTATCGCAATCGGCCTTGTTGACCGCTggg  <  1:2958895/69‑1 (MQ=255)
                                                                  |                                                                
GTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTATCGCAATCGGCCTTGTTGACCGCTGGG  >  minE/1976090‑1976220

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