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 1,369,997 G→A 53.1% S115S (TCG→TCA)  yohJ → conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,369,9970GA53.1% 8.6 / 116.4 130S115S (TCG→TCA) yohJconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base G (17/44);  new base A (46/23);  total (63/67)
Fisher's exact test for biased strand distribution p-value = 1.08e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

Only 100 of 130 total aligned reads displayed.

CCCGGTAGTGGTTTCCTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGAAT  >  minE/1369934‑1370059
                                                               |                                                              
cccGGTAGTGGTTTCCTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAAc                                                            <  1:3098930/68‑1 (MQ=255)
    gTAGTGGTTTCCTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTa                                                       <  1:3087438/69‑1 (MQ=255)
    gTAGTGGTTTCCTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTa                                                       <  1:2136376/69‑1 (MQ=255)
       gTGGTTTCCTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTacac                                                    <  1:2896638/69‑1 (MQ=255)
       gTGGTTTCCTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTacac                                                    <  1:2141637/69‑1 (MQ=255)
       gTGGTTTCCTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTacac                                                    <  1:51496/69‑1 (MQ=255)
               cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:583612/66‑1 (MQ=255)
               cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:3259567/66‑1 (MQ=255)
               cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:177681/66‑1 (MQ=255)
               cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:2066405/66‑1 (MQ=255)
               cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:1633134/66‑1 (MQ=255)
               cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:3297864/66‑1 (MQ=255)
               cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:2202135/66‑1 (MQ=255)
               cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:2223321/66‑1 (MQ=255)
               cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:3160189/66‑1 (MQ=255)
               cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:138818/66‑1 (MQ=255)
               cTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:45723/66‑1 (MQ=255)
                tgtgCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:2943720/65‑1 (MQ=255)
                 gtgCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTa                                          <  1:106032/69‑1 (MQ=255)
                        cagtACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAAc                                             >  1:2713176/1‑59 (MQ=255)
                        cagtACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCg                                    >  1:347763/1‑68 (MQ=255)
                        cagtACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGt                                   >  1:1488706/1‑69 (MQ=255)
                        cagtACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGt                                   >  1:1252767/1‑69 (MQ=255)
                        cagtACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGt                                   >  1:876069/1‑69 (MQ=255)
                        cagtACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGt                                   >  1:527654/1‑69 (MQ=255)
                            aCGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGc                                                               <  1:3140615/37‑1 (MQ=255)
                            aCGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGc                                                               <  1:2909581/37‑1 (MQ=255)
                             cGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAg                                 >  1:469742/1‑66 (MQ=255)
                             cGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAg                                 >  1:2967463/1‑66 (MQ=255)
                             cGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAg                                 >  1:1132851/1‑66 (MQ=255)
                               cTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAg                            <  1:1871368/69‑1 (MQ=255)
                               cTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAg                            <  1:1492862/69‑1 (MQ=255)
                                   tggtTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTacac                                                    <  1:666855/41‑1 (MQ=255)
                                   tagtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:1596170/44‑1 (MQ=38)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAgg                       <  1:3287551/69‑1 (MQ=255)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAgg                       <  1:1584729/69‑1 (MQ=255)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:89552/45‑1 (MQ=38)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:665922/45‑1 (MQ=38)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:485352/45‑1 (MQ=38)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:1026856/45‑1 (MQ=38)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:921375/45‑1 (MQ=38)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGa                                               <  1:2141533/45‑1 (MQ=38)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                         >  1:2040690/1‑51 (MQ=39)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                         >  1:907923/1‑51 (MQ=39)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                         >  1:2683452/1‑51 (MQ=39)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                         >  1:2375835/1‑51 (MQ=39)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                         >  1:3018500/1‑51 (MQ=39)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                         >  1:840582/1‑51 (MQ=39)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                         >  1:2991254/1‑51 (MQ=39)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                         >  1:2364335/1‑51 (MQ=39)
                                    ggtTTTTCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTaa                                         >  1:1475260/1‑51 (MQ=39)
                                     gtTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTaca                                                     <  1:1243353/38‑1 (MQ=255)
                                     gtTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTaca                                                     <  1:507822/38‑1 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:2469479/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:3173036/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:2984133/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:3147802/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:3111405/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:770222/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:1058376/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:1134004/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:1208561/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:1602888/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:1613635/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:1839338/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:184611/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:2054658/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:2141376/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:2292687/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:2419747/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:2493303/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:2756228/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:831434/1‑68 (MQ=255)
                                        tttCTGGTGGTGAGCTGGAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATc                    >  1:279916/1‑68 (MQ=255)
                                           cTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCaga                 <  1:2396221/68‑1 (MQ=255)
                                           cTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCaga                 <  1:2919795/68‑1 (MQ=255)
                                                   gAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAatgatg        <  1:2637450/69‑1 (MQ=255)
                                                   gAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAatgatg        <  1:3280310/69‑1 (MQ=255)
                                                   gAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAatgatg        <  1:27846/69‑1 (MQ=255)
                                                   gAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAatgatg        <  1:1036224/69‑1 (MQ=255)
                                                    aGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAatgatg        >  1:1258302/1‑68 (MQ=255)
                                                      cTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg     <  1:992505/69‑1 (MQ=255)
                                                      cTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg     <  1:961374/69‑1 (MQ=255)
                                                      cTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg     <  1:413706/69‑1 (MQ=255)
                                                      cTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg     <  1:317570/69‑1 (MQ=255)
                                                      cTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg     <  1:1744752/69‑1 (MQ=255)
                                                       tGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg     <  1:3237478/68‑1 (MQ=255)
                                                       tGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGa    <  1:1153813/69‑1 (MQ=255)
                                                       tGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGa    <  1:1340443/69‑1 (MQ=255)
                                                       tGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGa    <  1:1430406/69‑1 (MQ=255)
                                                       tGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGa    <  1:2491961/69‑1 (MQ=255)
                                                       tGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGa    <  1:2900044/69‑1 (MQ=255)
                                                        ggAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGa    <  1:2603624/68‑1 (MQ=255)
                                                        ggAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGa    <  1:2886564/68‑1 (MQ=255)
                                                        ggAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGCATGATGGCGaa   >  1:464458/1‑69 (MQ=255)
                                                        ggAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGaa   >  1:809442/1‑69 (MQ=255)
                                                        ggAGTTCACAACTGGTGCACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGaa   >  1:2778084/1‑69 (MQ=255)
                                                         gAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCg     <  1:2774888/66‑1 (MQ=255)
                                                         gAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGAat  >  1:2804914/1‑69 (MQ=255)
                                                         gAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGAat  >  1:3359063/1‑69 (MQ=255)
                                                               |                                                              
CCCGGTAGTGGTTTCCTGTGCAGTCAGTACGCTGGTGGTTTTTCTGGTGGTGAGCTGGAGTTCGCAACTGGTACACGGTGAACGTAAAGTCGTAGGTCAGAAAGGATCAGAAGAATGATGGCGAAT  >  minE/1369934‑1370059

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