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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,569,883 C→T 23.1% S51S (AGC→AGT)  yibI → predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,569,8830CT23.1% 182.8 / 50.8 95S51S (AGC→AGT) yibIpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (41/32);  new base T (12/10);  total (53/42)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

TCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTGG  >  minE/2569813‑2569951
                                                                      |                                                                    
tCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGc                                                                      <  1:149024/71‑1 (MQ=255)
 cccTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGcc                                                                     >  1:843393/1‑71 (MQ=255)
 cccTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGcc                                                                     >  1:842159/1‑71 (MQ=255)
 cccTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGcc                                                                     >  1:3491670/1‑71 (MQ=255)
  ccTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCt                                                                    <  1:1558395/71‑1 (MQ=255)
     taccTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                                                                 >  1:111463/4‑71 (MQ=255)
         tGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTAcg                                                             >  1:3510562/1‑70 (MQ=255)
           aTTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTa                                                               <  1:971577/67‑1 (MQ=255)
           aTTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTActgt                                                           >  1:2019885/1‑69 (MQ=255)
           aTTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTActct                                                           >  1:3013801/1‑71 (MQ=255)
            tttccAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTg                                                          >  1:3710796/4‑71 (MQ=255)
             tGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTg                                                          <  1:524203/70‑1 (MQ=255)
               ccAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGc                                                         <  1:3466348/69‑1 (MQ=255)
               ccAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCAt                                                       >  1:3241722/1‑71 (MQ=255)
                 aaaaaaCGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                                                                 >  1:2014367/1‑59 (MQ=255)
                 aaaaaaCGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                                                                 >  1:3375704/1‑59 (MQ=255)
                 aaaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                                                     >  1:564705/1‑71 (MQ=255)
                  aaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                                                     >  1:937618/1‑70 (MQ=255)
                   aaaaCGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                                                                 >  1:2508762/1‑57 (MQ=255)
                   aaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTa                                                   >  1:3159904/1‑71 (MQ=255)
                    aaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTa                                                   >  1:2022477/1‑70 (MQ=255)
                    aaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTAt                                                  <  1:890090/71‑1 (MQ=255)
                     aGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc                                                 >  1:3358137/1‑71 (MQ=255)
                     aGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc                                                 <  1:985524/71‑1 (MQ=255)
                     aGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc                                                 <  1:1049032/71‑1 (MQ=255)
                      gcgcAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGc                                                                      >  1:2446425/1‑49 (MQ=255)
                        gcAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTg                                               <  1:2839573/70‑1 (MQ=255)
                         cAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGc                                             <  1:1188419/71‑1 (MQ=255)
                           atcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGcc                                            <  1:425152/68‑1 (MQ=255)
                           aCCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCg                                           >  1:188367/1‑71 (MQ=255)
                            ccATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGt                                          >  1:415982/1‑71 (MQ=255)
                             cATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGtt                                         >  1:948653/1‑71 (MQ=255)
                              aTCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGttt                                        >  1:2523582/1‑71 (MQ=255)
                              aTCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGtt                                         <  1:1663610/70‑1 (MQ=255)
                              aTCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATATGGCCGtt                                         <  1:2218898/70‑1 (MQ=255)
                               tCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTc                                       <  1:1351690/71‑1 (MQ=255)
                               tCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTc                                       <  1:2416691/71‑1 (MQ=255)
                                  ccATGCCGACGCTATTAATACGGCGGGCTGGGTGAGCCTGCTTACTCTGCATGtt                                                    <  1:2461933/55‑1 (MQ=255)
                                   cATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCtgtg                                   <  1:1107913/71‑1 (MQ=255)
                                   cATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCt                                                >  1:1243315/1‑58 (MQ=255)
                                    aTGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTAt                                                  >  1:1085642/1‑55 (MQ=255)
                                    aTGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCtgtg                                   >  1:3549510/1‑70 (MQ=255)
                                     tGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTActct                                                           >  1:3891268/1‑45 (MQ=255)
                                     tGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGt                                          >  1:1016108/1‑62 (MQ=255)
                                     tGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTgg                                  <  1:3709517/70‑1 (MQ=255)
                                        cGACGCTATTCATACGGCGGGCTGGGTGAGCCTGt                                                                  >  1:377072/1‑35 (MQ=255)
                                         gACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTtgt                                    <  1:2100924/64‑1 (MQ=255)
                                         gACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGATTTg                             <  1:611473/71‑1 (MQ=255)
                                         gACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGATTTg                             <  1:2600880/71‑1 (MQ=255)
                                         gACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGATTTg                             <  1:3418814/71‑1 (MQ=255)
                                          aCGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTg                                                          >  1:2800461/1‑41 (MQ=255)
                                          aCGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTg                                                          >  1:3411234/1‑41 (MQ=255)
                                          aCGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGc                                                         <  1:2571869/42‑1 (MQ=255)
                                          aCGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGc                                                         <  1:1838883/42‑1 (MQ=255)
                                          aCGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTgg                            >  1:1384040/1‑71 (MQ=255)
                                            gCTATTCATACGGCGGGCTGGGTGAGCCTGTTTTCTCTGCATGTTATCt                                                >  1:172294/1‑49 (MQ=255)
                                              tATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGAt                                >  1:3457178/1‑63 (MQ=255)
                                              tATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGAt                                >  1:3461707/1‑63 (MQ=255)
                                               aTTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGa                        >  1:3498529/1‑70 (MQ=255)
                                                ttCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACg                      >  1:1590569/1‑71 (MQ=255)
                                                ttCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACg                      >  1:3337287/1‑71 (MQ=255)
                                                ttCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATCTTAt                                                  >  1:3624033/1‑43 (MQ=255)
                                                 tCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGcc                                            <  1:137562/48‑1 (MQ=255)
                                                  cATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTAt                                                  >  1:3509457/1‑41 (MQ=255)
                                                   aTACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGc                          <  1:3270038/64‑1 (MQ=255)
                                                   aTACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGctc                   <  1:381442/71‑1 (MQ=255)
                                                   aTACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGctc                   >  1:3766557/1‑71 (MQ=255)
                                                    tACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGctct                  <  1:3087948/71‑1 (MQ=255)
                                                     aCGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGctct                  >  1:3399315/1‑70 (MQ=255)
                                                     aCGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTa                 >  1:2907231/1‑71 (MQ=255)
                                                      cggcggGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGctc                   >  1:3786883/1‑68 (MQ=255)
                                                      cggcggGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGctc                   >  1:1410986/1‑68 (MQ=255)
                                                      cggcggGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGctc                   >  1:840233/1‑68 (MQ=255)
                                                       ggcggGCTGGGTGAGCCTGTTTACTCTGCATGTTAt                                                  >  1:186579/1‑36 (MQ=255)
                                                        gcggGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTgg                                  >  1:3936005/1‑51 (MQ=255)
                                                        gcggGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCa              <  1:2277035/71‑1 (MQ=255)
                                                         cggGCTGGGTGAGCCTGTTTACTCTGCATGTTATc                                                 <  1:783882/35‑1 (MQ=255)
                                                          gggCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCtgt                                    <  1:3629224/47‑1 (MQ=255)
                                                           ggCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAAcc           <  1:1521807/71‑1 (MQ=255)
                                                            gttGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGATTTGGGCCACGCTTTa                 >  1:1399135/3‑64 (MQ=255)
                                                              tGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTgg                                  >  1:2417065/1‑45 (MQ=255)
                                                              tGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGATTTGGGCCACGCTTTa                 >  1:935435/1‑62 (MQ=255)
                                                              tGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCg          >  1:2309242/1‑69 (MQ=255)
                                                               gggTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt                                      <  1:3578078/40‑1 (MQ=255)
                                                               gggTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt                                      <  1:1408607/40‑1 (MQ=255)
                                                               gggTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt                                      <  1:2314624/40‑1 (MQ=255)
                                                               gggTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt                                      <  1:3725711/40‑1 (MQ=255)
                                                               gggTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTg                             <  1:727625/49‑1 (MQ=255)
                                                                ggTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAg       <  1:1096122/70‑1 (MQ=255)
                                                                ggTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGc      >  1:619740/1‑71 (MQ=255)
                                                                 gTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGATTTGGGCCACGCTTTACCGCCCGGAGCg     <  1:791423/71‑1 (MQ=255)
                                                                  tGAGTCTTTTTACGTTACATGTTATCTGGCCGttt                                        <  1:3703128/35‑1 (MQ=16)
                                                                  tGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCtg                                     <  1:3322792/38‑1 (MQ=255)
                                                                  tGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTAt                >  1:1754319/1‑59 (MQ=255)
                                                                  tGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGt    >  1:767200/1‑71 (MQ=255)
                                                                   gAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTtgtg                                   >  1:2382118/1‑39 (MQ=255)
                                                                   gAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGa                                 <  1:3575894/41‑1 (MQ=255)
                                                                    aGCCTGTTTACTCTGCTTGTTATCTGGCCGTTTCt                                      <  1:2753530/35‑1 (MQ=255)
                                                                    aGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTgg  >  1:2586938/1‑71 (MQ=255)
                                                                    aGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTgg  >  1:3481944/1‑71 (MQ=255)
                                                                      |                                                                    
TCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTCTATCAACCGGAGCGTGG  >  minE/2569813‑2569951

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A