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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,569,895 G→A 27.8% L55L (CTG→CTA) ‡ yibI → predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,569,8950GA27.8% 206.7 / 88.5 133L55L (CTG→CTA) ‡yibIpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base G (50/46);  new base A (17/20);  total (67/66)
Fisher's exact test for biased strand distribution p-value = 5.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 136 total aligned reads displayed.

TTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTGGCTGGGGTA  >  minE/2569825‑2569959
                                                                      |                                                                
ttGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTg                                                                  <  1:4366441/71‑1 (MQ=255)
ttGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTg                                                                  >  1:1663345/1‑71 (MQ=255)
 tGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTg                                                                  >  1:992449/1‑70 (MQ=255)
     aaaaaaCGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGt                                                             >  1:2334898/1‑71 (MQ=255)
     aaaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                                                             >  1:3214145/1‑71 (MQ=255)
     aaaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                                                             >  1:660056/1‑71 (MQ=255)
     aaaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                                                             >  1:1269569/1‑71 (MQ=255)
      aaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                                                             >  1:722329/1‑70 (MQ=255)
      aaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                                                             >  1:435764/1‑70 (MQ=255)
      aaaaACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGt                                                             >  1:4942626/1‑70 (MQ=255)
        aaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTAt                                                          >  1:1535867/1‑71 (MQ=255)
        aaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTAt                                                          >  1:1164799/1‑71 (MQ=255)
         aGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc                                                         <  1:5631368/71‑1 (MQ=255)
         aGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc                                                         <  1:22948/71‑1 (MQ=255)
          gcgcAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCt                                                        <  1:79918/71‑1 (MQ=255)
              aaCCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc                                                         <  1:3414335/66‑1 (MQ=255)
               atcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTa                                                           >  1:1354295/3‑63 (MQ=255)
                tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTa                                                           <  1:2660539/61‑1 (MQ=255)
                tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTa                                                           <  1:1396186/61‑1 (MQ=255)
                tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTa                                                           <  1:5340909/61‑1 (MQ=255)
                tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTAt                                                          >  1:3518308/2‑63 (MQ=255)
                tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGt                                                  <  1:1009023/70‑1 (MQ=255)
                ccATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGt                                                  <  1:4374643/71‑1 (MQ=255)
                ccATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGt                                                  <  1:515595/71‑1 (MQ=255)
                ccATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGt                                                  <  1:5276981/71‑1 (MQ=255)
                ccATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGt                                                  <  1:660972/71‑1 (MQ=255)
                 cATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGt                                                             >  1:2114441/1‑59 (MQ=255)
                  aTCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGtt                                                            >  1:3210049/1‑59 (MQ=255)
                  aTCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGtt                                                 >  1:4722256/1‑70 (MQ=255)
                   tCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGttt                                                <  1:2742562/70‑1 (MQ=255)
                   tCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTc                                               <  1:1489890/71‑1 (MQ=255)
                   tCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTc                                               <  1:1196356/71‑1 (MQ=255)
                     ctcATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTtg                                             >  1:2797549/3‑71 (MQ=255)
                     cccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCtg                                             <  1:2518199/71‑1 (MQ=255)
                     cccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt                                              <  1:3899699/70‑1 (MQ=255)
                     cccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt                                              <  1:3068120/70‑1 (MQ=255)
                      tcATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTa                                                           <  1:2215821/55‑1 (MQ=255)
                      tcATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGttttt                                              <  1:3591591/68‑3 (MQ=255)
                       cATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt                                              <  1:1049063/68‑1 (MQ=255)
                       cATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTtgtg                                           >  1:4692436/1‑71 (MQ=255)
                        aTGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTtg                                             <  1:5633290/68‑1 (MQ=255)
                        aTGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTgg                                          <  1:1260818/71‑1 (MQ=255)
                          gCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGttttt                                              >  1:1053594/1‑63 (MQ=255)
                          gCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTtg                                             >  1:1212457/1‑66 (MQ=255)
                          gCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTtg                                             >  1:5564650/1‑66 (MQ=255)
                          gCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGAt                                        >  1:5610432/1‑71 (MQ=255)
                           ccGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGAt                                        >  1:1878292/1‑70 (MQ=255)
                            cGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGAttt                                      <  1:2189882/71‑3 (MQ=255)
                             gACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTg                                     <  1:912649/71‑1 (MQ=255)
                               cGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGATTTggg                                   <  1:3254356/71‑1 (MQ=255)
                                    ttCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGtt                                                            <  1:4987888/41‑1 (MQ=255)
                                     tCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc                                                         <  1:5308913/43‑1 (MQ=255)
                                      cATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACg                              >  1:4651877/1‑69 (MQ=255)
                                      cATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGc                             >  1:876759/1‑70 (MQ=255)
                                       aTACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGtt                                                            <  1:4698348/38‑1 (MQ=255)
                                       aTACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGtt                                                            <  1:2048063/38‑1 (MQ=255)
                                       aTACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGtt                                                            <  1:4225046/38‑1 (MQ=255)
                                       aTACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGtt                                                            <  1:35103/38‑1 (MQ=255)
                                         aCGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTc                                               <  1:49556/49‑1 (MQ=255)
                                          cggcggGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGcc                                                    >  1:2241659/1‑43 (MQ=255)
                                          cggcggGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGcc                                                    >  1:5406819/1‑43 (MQ=255)
                                          cggcggGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGcc                                                    >  1:4706747/1‑43 (MQ=255)
                                          cggcggGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTc                                               >  1:3899144/1‑48 (MQ=255)
                                            gcggGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGcca                                >  1:4891553/1‑59 (MQ=255)
                                                gttGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTtgtg                                           <  1:4017103/44‑1 (MQ=255)
                                                gttGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTtgtg                                           <  1:1668426/44‑1 (MQ=255)
                                                gttGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGATTTGGGCCACGCTTTa                         >  1:4930081/3‑64 (MQ=255)
                                                gCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGa                                >  1:1167625/1‑57 (MQ=255)
                                                gCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGAGCGACg                              <  1:734327/59‑1 (MQ=255)
                                                   gggTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTgg                                          <  1:4455985/44‑1 (MQ=255)
                                                   gggTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAg               >  1:5049589/1‑71 (MQ=255)
                                                    ggTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGATTTGGGCCACGCTTTACCGCCCGGAg               <  1:408269/70‑1 (MQ=255)
                                                      tGAGTCTTTTTACGTTACATGTTATCTGGCCGttt                                                <  1:3095838/35‑1 (MQ=16)
                                                      tGAGTCTTTTTACGTTACATGTTATCTGGCCGttt                                                <  1:5563595/35‑1 (MQ=16)
                                                       gAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGAtt                                       <  1:4228381/43‑2 (MQ=255)
                                                       gAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGATTTGGGCCACGCTTTACCGCCCGGAGCggg           >  1:2862595/1‑69 (MQ=255)
                                                       gAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTg           >  1:2055722/1‑71 (MQ=255)
                                                        aGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCtgtg                                           >  1:24931/1‑38 (MQ=255)
                                                        aGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCtgtg                                           >  1:2650144/1‑38 (MQ=255)
                                                        aGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTgg          >  1:1817937/1‑71 (MQ=255)
                                                        aGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTg           <  1:4988941/70‑1 (MQ=255)
                                                        aGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTg           <  1:179309/70‑1 (MQ=255)
                                                            tGTTTAGTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTGGCTgg      >  1:738884/1‑71 (MQ=255)
                                                            tGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTGGCTg       <  1:264557/70‑1 (MQ=255)
                                                             gTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATc                                       >  1:2290054/1‑37 (MQ=255)
                                                             gTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGt            <  1:3236798/64‑1 (MQ=255)
                                                             gTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTGGCTggg     >  1:4756302/1‑71 (MQ=255)
                                                              tttACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTGGCTgggg    <  1:688267/71‑1 (MQ=255)
                                                              tttACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTGGCTgggg    <  1:3236960/71‑1 (MQ=255)
                                                              tttACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTGGCTgggg    <  1:2954639/71‑1 (MQ=255)
                                                               ttACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGa                                >  1:1526812/1‑42 (MQ=255)
                                                               ttACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGa                                >  1:1318107/1‑42 (MQ=255)
                                                               ttACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGa                                >  1:4199155/1‑42 (MQ=255)
                                                               ttACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGa                                >  1:3554903/1‑42 (MQ=255)
                                                               ttACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGc              >  1:4911116/1‑60 (MQ=255)
                                                               ttACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGc              >  1:3863784/1‑60 (MQ=255)
                                                                tACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAAc                    >  1:4468382/1‑53 (MQ=255)
                                                                tACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAAc                    >  1:976676/1‑53 (MQ=255)
                                                                  ctctGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCgg                 <  1:4119199/54‑1 (MQ=255)
                                                                     tGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTa                         <  1:4915046/43‑1 (MQ=255)
                                                                      |                                                                
TTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTGGCTGGGGTA  >  minE/2569825‑2569959

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