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 608,985 C→T 15.8% P423P (CCG→CCA)  pflB ← pyruvate formate lyase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE608,9850CT15.8% 293.5 / 39.7 120P423P (CCG→CCA) pflBpyruvate formate lyase I
Reads supporting (aligned to +/- strand):  ref base C (39/62);  new base T (10/9);  total (49/71)
Fisher's exact test for biased strand distribution p-value = 3.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.14e-01

Only 100 of 129 total aligned reads displayed.

GCGTACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCA  >  minE/608917‑609054
                                                                    |                                                                     
gCGTACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCg                                                                      <  1:3931339/70‑1 (MQ=255)
 cGTACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCggg                                                                    >  1:1808979/1‑71 (MQ=255)
  gTACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGc                                                                   >  1:1335388/1‑71 (MQ=255)
   tACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCt                                                                  <  1:1903957/71‑1 (MQ=255)
     cAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTa                                                                <  1:3093794/71‑1 (MQ=255)
       gCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCggg                                                                    <  1:1882474/65‑1 (MQ=255)
       gCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCgg                                                                     >  1:3197307/1‑64 (MQ=255)
          tGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACgcag                                                           >  1:2136562/1‑71 (MQ=255)
           cgTTTTCGCCAGGTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACgcag                                                           <  1:1296101/69‑1 (MQ=255)
           cgTTTTCGCCAGGTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACgcag                                                           >  1:3598461/2‑70 (MQ=255)
            gTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTAcgccgc                                                          <  1:1695153/70‑1 (MQ=255)
            gTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACgcagca                                                         <  1:256287/71‑1 (MQ=255)
             ttttCGCCAGGTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACgcagcag                                                        >  1:3433081/1‑70 (MQ=255)
              tttCGCCAGGTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACgcagcagg                                                       >  1:3199830/1‑69 (MQ=255)
               ttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAAGGATCATCGGGCTTACGCagcaag                                                       >  1:1778673/1‑70 (MQ=255)
               ttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCgg                                                                     >  1:3470676/1‑56 (MQ=255)
               ttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaag                                                       >  1:527550/1‑70 (MQ=255)
                tCGCCAGGTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCagcaggc                                                      >  1:3820084/1‑70 (MQ=255)
                   ccAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATa                                                  <  1:2004439/71‑1 (MQ=255)
                    cAGGTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAAtcg                                                 <  1:2406376/71‑3 (MQ=255)
                     aGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGc                                                >  1:746943/1‑71 (MQ=255)
                     aGGTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGc                                                >  1:1523287/1‑71 (MQ=255)
                      ggTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCATCAAGCAATAGCg                                               >  1:3409611/1‑71 (MQ=255)
                      ggTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCg                                               >  1:1617089/1‑71 (MQ=255)
                      ggTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATcgcg                                               >  1:584689/1‑71 (MQ=255)
                        tttGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCg                                               <  1:3466562/69‑1 (MQ=255)
                          tGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAg                                            <  1:1345190/70‑1 (MQ=255)
                          tGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGt                                           >  1:1450037/1‑71 (MQ=255)
                            cACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCa                                         >  1:1887477/1‑71 (MQ=255)
                            cACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCa                                         >  1:1403558/1‑71 (MQ=255)
                             aCGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAgcaagcaa                                                    <  1:430575/59‑1 (MQ=255)
                             aCGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAgcaagcaa                                                    <  1:435288/59‑1 (MQ=255)
                              cgtgcACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTc                                       <  1:3689070/68‑1 (MQ=255)
                              cgcgCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATc                                       <  1:2905324/71‑1 (MQ=255)
                              cgcgCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATc                                       <  1:3810445/71‑1 (MQ=255)
                               gtgcACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTaa                                            >  1:3461263/3‑64 (MQ=255)
                               gcgcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCg                                      <  1:2264441/71‑1 (MQ=255)
                                cgcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCt                                                                  >  1:238756/1‑42 (MQ=255)
                                 gcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgtt                                    <  1:2275509/71‑1 (MQ=255)
                                  cACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCgctg                                   <  1:444757/71‑1 (MQ=255)
                                   aCCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCgctgt                                  <  1:1484372/71‑1 (MQ=255)
                                     caaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCgctgtt                                 >  1:2861963/3‑70 (MQ=255)
                                     cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACgcag                                                           >  1:3632553/1‑44 (MQ=255)
                                     cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                                <  1:404777/71‑1 (MQ=255)
                                     cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGAAAGCAATAGCGTAGTCATCGttgttg                                <  1:76445/71‑1 (MQ=255)
                                     cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGAAAGCAATAGCGTAGTCATCGttgttg                                <  1:3363081/71‑1 (MQ=255)
                                      gaagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                                >  1:2659473/1‑70 (MQ=255)
                                      gaagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGa                               <  1:2835979/71‑1 (MQ=255)
                                       aagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACg                                                              >  1:2513884/1‑39 (MQ=255)
                                       aagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACg                                                              >  1:3085477/1‑39 (MQ=255)
                                       aagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaagca                                                     <  1:2171720/48‑1 (MQ=255)
                                       aagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                                >  1:2354153/1‑69 (MQ=255)
                                        agaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGaa                              >  1:3119929/1‑70 (MQ=255)
                                         gaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgt                                  <  1:909458/65‑1 (MQ=255)
                                         gaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgt                                  <  1:1567467/65‑1 (MQ=255)
                                         gaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGt                            >  1:2804005/1‑71 (MQ=255)
                                         gaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGt                            <  1:3833286/71‑1 (MQ=255)
                                         gaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGt                            <  1:3471068/71‑1 (MQ=255)
                                         gaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGt                            <  1:2244575/71‑1 (MQ=255)
                                         gaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGt                            <  1:2700263/71‑1 (MQ=255)
                                          aaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCg                                               <  1:264776/51‑1 (MQ=255)
                                          aaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCg                                               <  1:2014626/51‑1 (MQ=255)
                                          aaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCg                                               <  1:2019029/51‑1 (MQ=255)
                                          aaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTc                           <  1:1842783/71‑1 (MQ=255)
                                           aCTGCATTTGTTTAGCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgt                                  <  1:1304360/63‑1 (MQ=255)
                                           aCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgt                                  <  1:303174/63‑1 (MQ=255)
                                           aCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgt                                  <  1:1412339/63‑1 (MQ=255)
                                           aCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgt                                  <  1:1416918/63‑1 (MQ=255)
                                           aCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgt                                  <  1:2532501/63‑1 (MQ=255)
                                               cATTTGTTTACCAACGATCATCGGGCTTACgcagc                                                          <  1:1246759/35‑1 (MQ=255)
                                               cATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCgg                        <  1:785074/69‑1 (MQ=255)
                                               cATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCgg                        <  1:908338/69‑1 (MQ=255)
                                               cATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGAc                      >  1:1919654/1‑71 (MQ=255)
                                                 tttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCg                                               <  1:1631342/44‑1 (MQ=255)
                                                 tttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                                <  1:1793417/59‑1 (MQ=255)
                                                 tttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACg                     >  1:642692/1‑70 (MQ=255)
                                                  ttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGa                       >  1:3136309/1‑67 (MQ=255)
                                                  ttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCa                   >  1:1980019/1‑71 (MQ=255)
                                                   tGTTTACCAACGATCATCGGGCTTACGCAGCGAGCAATAGCGTa                                             >  1:592778/1‑44 (MQ=255)
                                                    gTTTACCAACGATCATCGGGCTTACGCagcaagca                                                     <  1:185198/35‑1 (MQ=255)
                                                    gTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCAt                  >  1:1297535/1‑70 (MQ=255)
                                                     tttACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttg                                   <  1:1340539/52‑1 (MQ=255)
                                                     tttACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATc                 <  1:2813371/70‑1 (MQ=255)
                                                       tACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGaa                              >  1:1184445/1‑55 (MQ=255)
                                                         ccAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGt             <  1:2234179/70‑1 (MQ=255)
                                                         ccAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTc            <  1:534087/71‑1 (MQ=255)
                                                          cAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCg                         >  1:1200391/1‑57 (MQ=255)
                                                            aCGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGa                       >  1:2558266/1‑57 (MQ=255)
                                                             cGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAgg              <  1:596952/65‑1 (MQ=255)
                                                             cGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg        <  1:1121057/71‑1 (MQ=255)
                                                             cGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg        <  1:3905242/71‑1 (MQ=255)
                                                             cGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg        <  1:3198513/71‑1 (MQ=255)
                                                              gATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGt       <  1:3827410/71‑1 (MQ=255)
                                                              gATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGt       <  1:1449555/71‑1 (MQ=255)
                                                                tcatcGGGCTTACGCAGCAAGCAATAGCGTAGTCa                                         >  1:469559/1‑35 (MQ=255)
                                                                  atcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtct    >  1:39150/1‑70 (MQ=255)
                                                                  atcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtct    >  1:2943661/1‑70 (MQ=255)
                                                                   tcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgtt                                    <  1:2213414/37‑1 (MQ=255)
                                                                   tcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGGCATCGTTCTCa  <  1:1346632/71‑1 (MQ=255)
                                                                    cGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCa  >  1:850367/1‑70 (MQ=255)
                                                                    |                                                                     
GCGTACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCA  >  minE/608917‑609054

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