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 2,189,346 A→G 32.3% H142H (CAT→CAC)  nanR ← DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,189,3460AG32.3% 87.8 / 57.3 108H142H (CAT→CAC) nanRDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base A (20/53);  new base G (16/19);  total (36/72)
Fisher's exact test for biased strand distribution p-value = 8.08e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01

Only 100 of 109 total aligned reads displayed.

GTTATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAATTGTTCGAAATGGGCAAT  >  minE/2189280‑2189411
                                                                  |                                                                 
gttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:1004281/69‑1 (MQ=255)
gttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:2121537/69‑1 (MQ=255)
gttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:2621566/69‑1 (MQ=255)
gttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:2636421/69‑1 (MQ=255)
gttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:2786914/69‑1 (MQ=255)
gttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:1825374/69‑1 (MQ=255)
gttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:3047510/69‑1 (MQ=255)
gttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:340271/69‑1 (MQ=255)
gttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:470169/69‑1 (MQ=255)
gttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:609459/69‑1 (MQ=255)
gttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:637746/69‑1 (MQ=255)
gttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:1190956/69‑1 (MQ=255)
gttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:827469/69‑1 (MQ=255)
 ttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:2071511/68‑1 (MQ=255)
 ttATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:951301/68‑1 (MQ=255)
      cAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGc                                                           >  1:263513/1‑69 (MQ=255)
        gCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCg                                                         <  1:2554459/69‑1 (MQ=255)
              gactgTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTg                                                                 <  1:658129/55‑1 (MQ=255)
                 tgTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAgcgc                                                 <  1:1644689/68‑1 (MQ=255)
                 tgTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAgcgc                                                 <  1:1647682/68‑1 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTTCTCATCGGTGGCATGTTCAGCCg                                                         >  1:3286519/1‑56 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGcc                                                          >  1:3100707/1‑55 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCg                                                         >  1:701595/1‑56 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCg                                                         >  1:2604447/1‑56 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCg                                                         >  1:187915/1‑56 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCg                                                         >  1:1877253/1‑56 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCg                                                         >  1:790590/1‑56 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCg                                                         >  1:2794065/1‑56 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCg                                                         >  1:178439/1‑56 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCg                                                         >  1:759928/1‑56 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCg                                                         >  1:362378/1‑56 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCg                                                         >  1:411399/1‑56 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCg                                                         >  1:1280539/1‑56 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCa                                                       >  1:1140108/1‑58 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCa                                             <  1:271570/68‑1 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCa                                             <  1:182316/68‑1 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAg                                            <  1:1431316/69‑1 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAg                                            <  1:2406824/69‑1 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAg                                            <  1:311113/69‑1 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAg                                            <  1:2759280/69‑1 (MQ=255)
                     gATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCAACGGTGGCGTGTTCAGCCGCATAGCGCACCa                                             <  1:65945/68‑1 (MQ=255)
                        ttCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGAc                                          >  1:156115/1‑68 (MQ=255)
                        ttCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGAc                                          >  1:3183760/1‑68 (MQ=255)
                        ttCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGAc                                          >  1:2042111/1‑68 (MQ=255)
                           cAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTgg                                       <  1:2132654/68‑1 (MQ=255)
                           cAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTgg                                       <  1:1465435/68‑1 (MQ=255)
                                cTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTGTTCAGCCGCATAg                                                    >  1:89318/1‑50 (MQ=255)
                                cTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTGTTCAGCCGCATAGCGCACCAGGCTGGa                                      >  1:356733/1‑64 (MQ=255)
                                cTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTGTTCAGCCGCATAGCGCACCAGGCTGGAt                                     >  1:820929/1‑65 (MQ=255)
                                cTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTGTTCAGCCGCATAGCGCACCAGGCTGGAt                                     >  1:3410441/1‑65 (MQ=255)
                                cTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTGTTCAGCCGCATAGCGCACCAGGCTGGAt                                     >  1:981550/1‑65 (MQ=255)
                                cTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTGTTCAGCCGCATAGCGCACCAGGCTGGAt                                     >  1:364820/1‑65 (MQ=255)
                                cTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTGTTCAGCCGCATAGCGCACCAGGCTGGAt                                     >  1:2230445/1‑65 (MQ=255)
                                cTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTGTTCAGCCGCATAGCGCACCAGGCTGGAt                                     >  1:3171321/1‑65 (MQ=255)
                                cTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTGTTCAGCCGCATAGCGCACCAGGCTGGAt                                     >  1:3115246/1‑65 (MQ=255)
                                cTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTGTTCAGCCGCATAGCGCACCAGGCTGGAt                                     >  1:904576/1‑65 (MQ=255)
                                cTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTGTTCAGCCGCATAGCGCACCAGGCTGGAt                                     >  1:661873/1‑65 (MQ=255)
                                cTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTGTTCAGCCGCATAGCGCACCAGGCTGGAt                                     >  1:1831001/1‑65 (MQ=255)
                                cTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTGTTCAGCCGCATAGCGCACCAGGCTGGAt                                     >  1:869982/1‑65 (MQ=255)
                                cTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCGTGTTCAGCCGCATAGCGCACCAGGCTGGAt                                     >  1:1002669/1‑65 (MQ=255)
                                  tttGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAg                               <  1:3124598/69‑1 (MQ=255)
                                     gCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAg                               <  1:2648101/66‑1 (MQ=255)
                                     gCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGaa                             <  1:2923435/68‑1 (MQ=255)
                                     gCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGaa                             <  1:2413819/68‑1 (MQ=255)
                                     gCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGaa                             <  1:2028037/68‑1 (MQ=255)
                                     gCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGaa                             <  1:755865/68‑1 (MQ=255)
                                     gCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGaa                             <  1:1226582/68‑1 (MQ=255)
                                        aGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAg                          <  1:2933674/68‑1 (MQ=255)
                                        aGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAg                          <  1:2929973/68‑1 (MQ=255)
                                            aaTCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTa                     <  1:2140587/69‑1 (MQ=255)
                                            aaTCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTa                     <  1:101216/69‑1 (MQ=255)
                                            aaTCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTa                     <  1:1423674/69‑1 (MQ=255)
                                            aaTCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTa                     <  1:755203/69‑1 (MQ=255)
                                            aaTCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTa                     <  1:1407009/69‑1 (MQ=255)
                                            aaTCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTa                     <  1:2224951/69‑1 (MQ=255)
                                            aaTCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTa                     <  1:1767446/69‑1 (MQ=255)
                                            aaTCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTa                     <  1:2005175/69‑1 (MQ=255)
                                            aaTCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTa                     <  1:1993265/69‑1 (MQ=255)
                                              tCGATTTGCTCATCGGTGGCATGTTCAGGCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAAt                   <  1:1379771/69‑1 (MQ=255)
                                              tCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTa                     <  1:1367082/67‑1 (MQ=255)
                                              tCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAAt                   <  1:21633/69‑1 (MQ=255)
                                              tCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAAt                   <  1:3332798/69‑1 (MQ=255)
                                              tCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAAt                   <  1:944748/69‑1 (MQ=255)
                                              tCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAAt                   <  1:2509234/69‑1 (MQ=255)
                                              tCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAAt                   <  1:2049839/69‑1 (MQ=255)
                                              tCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAAt                   <  1:1123279/69‑1 (MQ=255)
                                              tCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAAt                   <  1:1315033/69‑1 (MQ=255)
                                              tCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAAt                   <  1:1375831/69‑1 (MQ=255)
                                              tCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAAt                   <  1:3281477/69‑1 (MQ=255)
                                              tCGATTTGCTCATCGGTGGCATGCTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAAt                   <  1:767534/69‑1 (MQ=255)
                                                            ggTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAg                               <  1:1568194/43‑1 (MQ=255)
                                                            ggTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAg                               <  1:958954/43‑1 (MQ=255)
                                                            ggTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAATTGTTCGAAATggg      >  1:2722101/1‑68 (MQ=255)
                                                            ggTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAATTGTTCGAAATggg      >  1:1157186/1‑68 (MQ=255)
                                                            ggTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAATTGTTCGAAATGGGc     <  1:2738566/69‑1 (MQ=255)
                                                            ggTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAATTGTTCGAAATGGGc     <  1:753931/69‑1 (MQ=255)
                                                            ggTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAATTGTTCGAAATGGGc     <  1:2623732/69‑1 (MQ=255)
                                                            ggTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAATTGTTCGAAATGGGc     <  1:926496/69‑1 (MQ=255)
                                                            ggTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAATTGTTCGAAATGGGc     <  1:371443/69‑1 (MQ=255)
                                                               ggCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAATTGTTCGAAATGGGCAAt  <  1:303644/69‑1 (MQ=255)
                                                                  |                                                                 
GTTATCCAGCGACTGACTGTTGATTTCCAGTGCTTTTGCCAGCAAATCGATTTGCTCATCGGTGGCATGTTCAGCCGCATAGCGCACCAGACTGGATTCAAAGAACAGACGTAATTGTTCGAAATGGGCAAT  >  minE/2189280‑2189411

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