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 1,370,006 A→G 54.9% V118V (GTA→GTG)  yohJ → conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,370,0060AG54.9% 27.1 / 101.5 125V118V (GTA→GTG) yohJconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base A (17/39);  new base G (45/23);  total (63/62)
Fisher's exact test for biased strand distribution p-value = 1.30e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 138 total aligned reads displayed.

GTAGTGGTTTCCTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGAATATCTGGTGGT  >  minE/1369938‑1370069
                                                                    |                                                               
gTAGTGGTTTCCTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTa                                                                 <  1:2136376/69‑1 (MQ=255)
gTAGTGGTTTCCTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTa                                                                 <  1:3087438/69‑1 (MQ=255)
   gTGGTTTCCTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTacac                                                              <  1:2896638/69‑1 (MQ=255)
   gTGGTTTCCTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTacac                                                              <  1:2141637/69‑1 (MQ=255)
           cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:3297864/66‑1 (MQ=255)
           cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:177681/66‑1 (MQ=255)
           cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:1609247/66‑1 (MQ=255)
           cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:2066405/66‑1 (MQ=255)
           cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:257795/66‑1 (MQ=255)
           cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:138818/66‑1 (MQ=255)
           cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:1253273/66‑1 (MQ=255)
           cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:45723/66‑1 (MQ=255)
           cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:3160189/66‑1 (MQ=255)
           cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:2223321/66‑1 (MQ=255)
            tgtgCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:2943720/65‑1 (MQ=255)
                    cagtACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCg                                              >  1:347763/1‑68 (MQ=255)
                    cagtACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGt                                             >  1:1252767/1‑69 (MQ=255)
                    cagtACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGt                                             >  1:3272586/1‑69 (MQ=255)
                    cagtACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGt                                             >  1:527654/1‑69 (MQ=255)
                         cGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAg                                           >  1:1132851/1‑66 (MQ=255)
                         cGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAg                                           >  1:2149945/1‑66 (MQ=255)
                           cTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAg                                      <  1:1492862/69‑1 (MQ=255)
                           cTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAg                                      <  1:1871368/69‑1 (MQ=255)
                               tggtTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTacac                                                              <  1:666855/41‑1 (MQ=255)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAgg                                 <  1:1584729/69‑1 (MQ=255)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAgg                                 <  1:3287551/69‑1 (MQ=255)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:486580/45‑1 (MQ=38)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:485352/45‑1 (MQ=38)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:89552/45‑1 (MQ=38)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:2141533/45‑1 (MQ=38)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:1026856/45‑1 (MQ=38)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                                         <  1:665922/45‑1 (MQ=38)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                                   >  1:2810772/1‑51 (MQ=39)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                                   >  1:2683452/1‑51 (MQ=39)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                                   >  1:2375835/1‑51 (MQ=39)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                                   >  1:2991254/1‑51 (MQ=39)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                                   >  1:3018500/1‑51 (MQ=39)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                                   >  1:2364335/1‑51 (MQ=39)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                                   >  1:907923/1‑51 (MQ=39)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                                   >  1:1475260/1‑51 (MQ=39)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                                   >  1:2040690/1‑51 (MQ=39)
                                ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                                   >  1:840582/1‑51 (MQ=39)
                                 gtTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTaca                                                               <  1:1243353/38‑1 (MQ=255)
                                 gtTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTaca                                                               <  1:507822/38‑1 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:3147802/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:3123470/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:919561/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:2984133/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:3173036/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:1602888/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:1613635/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:770222/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:1839338/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:279916/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:3324994/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:184611/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:1134004/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:2756228/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:2690831/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:1058376/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:2493303/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:2469479/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:2292687/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                              >  1:2419747/1‑68 (MQ=255)
                                    tttCTGGTGGTGAGCTGGAGTTCACAACTGGTCCACGGTGAACGTAAATTCGTAGGTc                                        >  1:2102733/1‑58 (MQ=255)
                                       cTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCaga                           <  1:2919795/68‑1 (MQ=255)
                                       cTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCaga                           <  1:2396221/68‑1 (MQ=255)
                                               gAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAatgatg                  <  1:1036224/69‑1 (MQ=255)
                                               gAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAatgatg                  <  1:1171345/69‑1 (MQ=255)
                                               gAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAatgatg                  <  1:2948726/69‑1 (MQ=255)
                                               gAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAatgatg                  <  1:27846/69‑1 (MQ=255)
                                               gAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAatgatg                  <  1:2637450/69‑1 (MQ=255)
                                                aGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAatgatg                  >  1:56853/1‑68 (MQ=255)
                                                  cTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg               <  1:426322/69‑1 (MQ=255)
                                                  cTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg               <  1:961374/69‑1 (MQ=255)
                                                  cTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg               <  1:992505/69‑1 (MQ=255)
                                                  cTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg               <  1:317570/69‑1 (MQ=255)
                                                  cTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg               <  1:1744752/69‑1 (MQ=255)
                                                   tGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg               <  1:3237478/68‑1 (MQ=255)
                                                   tGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGa              <  1:1340443/69‑1 (MQ=255)
                                                   tGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGa              <  1:2900044/69‑1 (MQ=255)
                                                   tGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGa              <  1:713266/69‑1 (MQ=255)
                                                   tGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGa              <  1:1919796/69‑1 (MQ=255)
                                                    ggAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGa              <  1:2886564/68‑1 (MQ=255)
                                                    ggAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCa                             >  1:1432331/1‑53 (MQ=255)
                                                    ggAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGCATGATGGCGaa             >  1:464458/1‑69 (MQ=255)
                                                    ggAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGaa             >  1:1098777/1‑69 (MQ=255)
                                                    ggAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGaa             >  1:862154/1‑69 (MQ=255)
                                                    ggAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGaa             >  1:1542900/1‑69 (MQ=255)
                                                    ggAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGaa             >  1:809442/1‑69 (MQ=255)
                                                    ggAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGaa             >  1:2778084/1‑69 (MQ=255)
                                                     gAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg               <  1:2774888/66‑1 (MQ=255)
                                                               cTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGAATATCTggtggt  <  1:2449604/69‑1 (MQ=255)
                                                               cTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGAATATCTggtggt  <  1:2862405/69‑1 (MQ=255)
                                                               cTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGAATATCTggtggt  <  1:3108157/69‑1 (MQ=255)
                                                               cTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGAATATCTggtggt  <  1:1358506/69‑1 (MQ=255)
                                                                    acacGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg               <  1:64599/51‑1 (MQ=255)
                                                                    acacGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg               <  1:381115/51‑1 (MQ=255)
                                                                    acacGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg               <  1:115463/51‑1 (MQ=255)
                                                                    acacGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg               <  1:3264721/51‑1 (MQ=255)
                                                                    |                                                               
GTAGTGGTTTCCTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGAATATCTGGTGGT  >  minE/1369938‑1370069

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