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 1,211,250 G→A 26.9% S34S (TCC→TCT)  cspC ← stress protein, member of the CspA‑family

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,211,2500GA26.9% 194.7 / 75.4 119S34S (TCC→TCT) cspCstress protein, member of the CspA‑family
Reads supporting (aligned to +/- strand):  ref base G (38/49);  new base A (9/23);  total (47/72)
Fisher's exact test for biased strand distribution p-value = 1.43e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 123 total aligned reads displayed.

GCCGTCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGA  >  minE/1211181‑1211320
                                                                     |                                                                      
  cGTCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGgag                                                                     <  1:3148808/71‑1 (MQ=255)
  cGTCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGgag                                                                     <  1:1933932/71‑1 (MQ=255)
   gTCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGgag                                                                     >  1:3579978/1‑70 (MQ=255)
    tCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGgag                                                                     >  1:854272/1‑69 (MQ=255)
    tCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGga                                                                      >  1:1729316/1‑68 (MQ=255)
     ccTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAg                                                                  >  1:2486325/1‑71 (MQ=255)
      cTGAATGTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAgt                                                                 >  1:739256/1‑71 (MQ=255)
       tGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAgtg                                                                >  1:57372/1‑71 (MQ=255)
       gtgaTTTCGAACTCTACGCGCTGACCTTCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAgtg                                                                <  1:3133154/68‑1 (MQ=255)
         aaTTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAgtg                                                                <  1:5304883/69‑1 (MQ=255)
         aaTTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTa                                                              <  1:5534542/71‑1 (MQ=255)
         aaTTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTa                                                              >  1:5393203/1‑71 (MQ=255)
          aTTTCGAACTCTACGCGCTGACCTTCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTAc                                                             >  1:1514981/1‑71 (MQ=255)
          aTTTCGAACTCTACGCGCTGACCTTCAGCAAGAGTTTCAAAACCATTAGTCTGGATTGCAGAGAAgtg                                                                <  1:1848828/68‑1 (MQ=255)
          aTTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTa                                                              <  1:5208823/70‑1 (MQ=255)
           tttCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACg                                                            <  1:394843/71‑1 (MQ=255)
           tttCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACg                                                            <  1:2215967/71‑1 (MQ=255)
           tttCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACg                                                            <  1:1315390/71‑1 (MQ=255)
           tttCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACg                                                            <  1:367860/71‑1 (MQ=255)
                aaCTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAgtg                                                                <  1:4910506/62‑1 (MQ=255)
                aaCTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAgtg                                                                <  1:2621380/62‑1 (MQ=255)
                aaCTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAaca                                                        >  1:202511/1‑70 (MQ=255)
                aaCTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAaca                                                        >  1:2992507/1‑70 (MQ=255)
                     aaCGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCtt                                                  >  1:4738548/1‑71 (MQ=255)
                      aCGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGgag                                                                     <  1:4306100/51‑1 (MQ=255)
                       cGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTtg                                                <  1:1692410/71‑1 (MQ=255)
                        tttCTGACCTTCGTCCAGAGATTTGTAACCATCGTTCTGGATAGCAgaga                                                                    <  1:3311892/49‑1 (MQ=255)
                        gcgcTGACCTTCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCttt                                                 <  1:59939/66‑1 (MQ=255)
                         ttCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTtgct                                              >  1:1588597/1‑71 (MQ=255)
                         cgcTGACCTTCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTtgc                                               <  1:5022279/68‑1 (MQ=255)
                          tCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTtgctg                                             >  1:4519688/1‑71 (MQ=255)
                           cTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTtgctgc                                            >  1:1254573/1‑71 (MQ=255)
                            tGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTtgctgc                                            >  1:468109/1‑70 (MQ=255)
                             gACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCa                                          >  1:5551196/1‑71 (MQ=255)
                                 ttCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTa                                                              <  1:1258506/47‑1 (MQ=255)
                                 ttCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTa                                                              <  1:138043/47‑1 (MQ=255)
                                 ttCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTa                                                              <  1:5523298/47‑1 (MQ=255)
                                  tCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGc                                     >  1:3933927/1‑71 (MQ=255)
                                  tCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGc                                     >  1:2276753/1‑71 (MQ=255)
                                  tCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCtt                                                  <  1:3821948/58‑1 (MQ=255)
                                  tCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCtt                                                  <  1:1788695/58‑1 (MQ=255)
                                  tCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCtt                                                  <  1:5328213/58‑1 (MQ=255)
                                   cAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGgaga                                                                    >  1:1257439/1‑39 (MQ=255)
                                   cAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTa                                                              >  1:574708/1‑45 (MQ=255)
                                   cAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAg                                      <  1:3489174/69‑1 (MQ=255)
                                   cAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGc                                     <  1:1600824/70‑1 (MQ=255)
                                    aGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCg                                   <  1:2632015/71‑1 (MQ=255)
                                      ccAGAGTTTTGAAGCCATTACCCTGGATAGCGgag                                                                     <  1:3270136/35‑1 (MQ=255)
                                       aagagTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAg                                >  1:2641007/2‑71 (MQ=255)
                                        agagTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGact                               <  1:2794389/71‑3 (MQ=255)
                                        agagTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAg                                >  1:5312850/1‑70 (MQ=255)
                                        agagTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGt                               <  1:1759384/71‑1 (MQ=255)
                                          agTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTaa                             <  1:5371059/71‑1 (MQ=255)
                                          agTTTTAAATCCATTAGTCTGGATTGCAGAGAAGTGTACGAac                                                         <  1:2637403/43‑1 (MQ=16)
                                          agTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTaa                             <  1:4061192/71‑1 (MQ=16)
                                           gTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                            <  1:2078635/71‑1 (MQ=255)
                                           gTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                            <  1:5075619/71‑1 (MQ=255)
                                           gTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                            >  1:2186337/1‑71 (MQ=255)
                                           gTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                            <  1:5394219/71‑1 (MQ=255)
                                           gTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAAt                            <  1:1547175/71‑1 (MQ=16)
                                             tttAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGccg                                          <  1:5545042/55‑2 (MQ=16)
                                              ttGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGa                          <  1:1533115/70‑1 (MQ=255)
                                              ttGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGa                          <  1:2655222/70‑1 (MQ=255)
                                                 aaaccATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAAcc                      <  1:663283/68‑1 (MQ=12)
                                                  aGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGcc                      >  1:431655/1‑70 (MQ=255)
                                                    ccATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCttt                                                 >  1:1058512/1‑41 (MQ=19)
                                                    ccATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaaa                   <  1:2066571/71‑1 (MQ=255)
                                                    ccATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaaa                   <  1:2245700/71‑1 (MQ=255)
                                                     cATTGCTCTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGa                                 >  1:3652710/1‑56 (MQ=2)
                                                     cATTGCTCTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGa                                 >  1:2481815/1‑56 (MQ=2)
                                                     cATTGCTCTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCaaa                   <  1:5092732/70‑1 (MQ=9)
                                                     cATTGCTCTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCaaa                   <  1:951577/70‑1 (MQ=9)
                                                     cATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGa                                 >  1:2581149/1‑56 (MQ=12)
                                                      aTTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                 >  1:597120/1‑71 (MQ=255)
                                                      aTTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                 >  1:3805245/1‑71 (MQ=255)
                                                       ttACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaa                    <  1:3383326/67‑1 (MQ=255)
                                                         aCCCTGGATAGCGGAGAAGTGTACGAACACATCtt                                                  <  1:4364757/35‑1 (MQ=255)
                                                         aCCCTGGATAGCGGAGAAGTGTACGAACACATCtt                                                  <  1:1814370/35‑1 (MQ=255)
                                                         aCCCTGGATAGCGGAGAAGTGTACGAACACATCtt                                                  <  1:2290882/35‑1 (MQ=255)
                                                         aCCCTGGATAGCGGAGAAGTGTACGAACACATCtt                                                  <  1:2382160/35‑1 (MQ=255)
                                                          gtcTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtt              <  1:1279319/68‑1 (MQ=12)
                                                          gtcTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtt              <  1:4722556/68‑1 (MQ=12)
                                                          ctcTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCAAAACCttt             <  1:2084618/69‑1 (MQ=9)
                                                          cccTGGATAGCGGAGAAGTGTAAGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCtt              <  1:4050024/70‑1 (MQ=255)
                                                           tcTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATcc                <  1:35234/66‑1 (MQ=12)
                                                            cTGGATAGCGGAGAAGTGTACGAACACATCTTTTCTGCCATCAGCCGGAGTAATGAAGCCAAAACCtt              >  1:2917133/1‑68 (MQ=255)
                                                            cTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAg           <  1:3836516/71‑1 (MQ=255)
                                                             tGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtt              >  1:4297971/1‑67 (MQ=12)
                                                             tGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGa          >  1:290164/1‑71 (MQ=255)
                                                              ggATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGAc         >  1:1426323/1‑71 (MQ=255)
                                                               gATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGa          >  1:4172713/1‑69 (MQ=255)
                                                               gATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACt        >  1:2843540/1‑71 (MQ=255)
                                                               gATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACt        <  1:523556/71‑1 (MQ=12)
                                                                   gCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGc                       >  1:3857525/1‑52 (MQ=255)
                                                                   gCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa            <  1:3655965/63‑1 (MQ=255)
                                                                   gCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGtt    <  1:153090/71‑1 (MQ=255)
                                                                    cGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTa                              <  1:1732270/44‑1 (MQ=255)
                                                                    cGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa            <  1:5060615/62‑1 (MQ=255)
                                                                     ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa  <  1:5539536/71‑1 (MQ=255)
                                                                     ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa  <  1:303111/71‑1 (MQ=255)
                                                                     |                                                                      
GCCGTCCTGAATTTCGAACTCAACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGA  >  minE/1211181‑1211320

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