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
A4 F1 I0 R1 70 84.3 4123603 97.0% 3999894 62.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,763,556 T→C 36.2% noncoding (288/1542 nt) rrsG ← 16S ribosomal RNA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,763,5560TC36.2% 130.1 / 143.9 130noncoding (288/1542 nt)rrsG16S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base T (43/40);  new base C (15/32);  total (58/72)
Fisher's exact test for biased strand distribution p-value = 4.28e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.70e-01

Only 100 of 131 total aligned reads displayed.

AGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGC  >  minE/1763501‑1763624
                                                       |                                                                    
aGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCtt                                                       >  1:1260961/1‑71 (MQ=31)
 ggAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTg                                                      <  1:3503745/71‑1 (MQ=17)
   aGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGt                                                    <  1:2921017/71‑1 (MQ=21)
   aGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGt                                                    <  1:1837853/71‑1 (MQ=21)
    gTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTg                                                   <  1:3411713/71‑1 (MQ=34)
    gTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATACTCTCAGACCAGCTAGGGATCGTCGCCTTg                                                      >  1:2489729/1‑68 (MQ=18)
     tCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGa                                                  <  1:887084/71‑1 (MQ=21)
       tGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGc                                                >  1:2794406/1‑71 (MQ=21)
         gACCGTGTCTCAGTTCCAGTTTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAg                                                 <  1:964485/68‑1 (MQ=11)
         gACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGcc                                               <  1:1359572/70‑1 (MQ=35)
          aCCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAg                                                 <  1:4106109/67‑1 (MQ=35)
          aCCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAg                                                 <  1:3765113/67‑1 (MQ=35)
          aCCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGt                                             <  1:275940/71‑1 (MQ=34)
          aCCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGt                                             <  1:1183851/71‑1 (MQ=34)
          aCCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGt                                             >  1:1354150/1‑71 (MQ=21)
           ccGTGTCTCAGTTCCAGTGTGGCTGGTTATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGtt                                            <  1:1499709/71‑1 (MQ=21)
           ccGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGtt                                            <  1:3894666/71‑1 (MQ=34)
           ccGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGtt                                            <  1:2601417/71‑1 (MQ=34)
           ccGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGt                                             >  1:3645304/1‑70 (MQ=35)
           ccGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGtt                                            <  1:638047/71‑1 (MQ=21)
           ccGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGtt                                            <  1:633282/71‑1 (MQ=21)
            cGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGt                                             <  1:329201/69‑1 (MQ=35)
             gtgtCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAc                                          >  1:1386387/1‑71 (MQ=34)
             gtgtCTCAGTTCCAGTGTGGCT‑GTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAcc                                         >  1:3618616/1‑71 (MQ=255)
                tctcAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAccc                                        <  1:3612557/70‑1 (MQ=35)
                tctcAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAccc                                        <  1:1119776/70‑1 (MQ=35)
                tctcAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTAcccc                                       <  1:4066828/71‑1 (MQ=21)
                 ctcAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCcca                                      >  1:3851990/1‑71 (MQ=34)
                 ctcAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCcca                                      >  1:1883158/1‑71 (MQ=34)
                    aGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGtt                                            >  1:18300/1‑62 (MQ=35)
                    aGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCccacc                                    >  1:2209441/1‑70 (MQ=35)
                    aGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCccacc                                    >  1:3648902/1‑70 (MQ=35)
                    aGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCccacc                                    >  1:2457982/1‑70 (MQ=35)
                    aGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCccacc                                    >  1:501426/1‑70 (MQ=35)
                    aGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCccacc                                    >  1:3527212/1‑70 (MQ=35)
                    aGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGTATCGTCGCCTTGGTGAGCCGTTACCccac                                     <  1:2906531/69‑1 (MQ=255)
                     gTTCCAGTGTGGCTGGTCATCCTCTCAGATCAGCTAGTGATCGTCGCCTTGGTg                                                   <  1:3924238/54‑1 (MQ=11)
                     gTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCccacca                                   <  1:1952653/70‑1 (MQ=255)
                     gTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaa                                  <  1:3535470/71‑1 (MQ=255)
                      ttCCAGTGGGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaac                                 <  1:3021798/71‑1 (MQ=255)
                       tCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTgg                                                     >  1:151164/1‑50 (MQ=38)
                       tCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAg                                                 >  1:479435/1‑54 (MQ=35)
                       tCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaac                                 >  1:1177886/1‑70 (MQ=40)
                       tCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaac                                 >  1:3924493/1‑70 (MQ=40)
                        ccAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCtt                                                       >  1:1085227/1‑47 (MQ=32)
                        ccAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGt                                             >  1:3401486/1‑57 (MQ=35)
                        ccAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaac                                 >  1:3117233/1‑69 (MQ=40)
                           gtgtGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaac                                 <  1:1980476/66‑1 (MQ=40)
                           gtgtGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaac                                 <  1:1129297/66‑1 (MQ=40)
                           gtgtGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaac                                 <  1:1142978/66‑1 (MQ=40)
                           gtgtGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCt                            <  1:937853/71‑1 (MQ=255)
                             gtgGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaacaa                               >  1:2167107/1‑66 (MQ=255)
                             gtgGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaacaa                               >  1:1029678/1‑66 (MQ=255)
                              tgGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAAt                         <  1:3003436/71‑1 (MQ=255)
                                 cTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATccc                      <  1:2540749/71‑1 (MQ=255)
                                 cTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATccc                      <  1:3835123/71‑1 (MQ=255)
                                  tGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCa                     >  1:2171842/1‑71 (MQ=255)
                                  tGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCa                     >  1:3737869/1‑71 (MQ=255)
                                  tGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCa                     >  1:1704677/1‑71 (MQ=255)
                                   ggTCGTCCTCTCAGACCAGCTACTGATCGTCGCCTTGGTGAGCCTTTACCTCACCAACTAGCTAAt                         <  1:2629238/66‑1 (MQ=11)
                                    gTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAcc                                         >  1:606521/1‑49 (MQ=38)
                                    gTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAcc                                         >  1:1323544/1‑49 (MQ=38)
                                    gTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCAt                    <  1:568736/70‑1 (MQ=255)
                                     tCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCt                  >  1:134152/1‑71 (MQ=255)
                                     tCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCt                  >  1:1240325/1‑71 (MQ=255)
                                     tCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCa                     <  1:3618344/68‑1 (MQ=255)
                                      cATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTg                 >  1:219992/1‑71 (MQ=255)
                                       aTCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTgg                <  1:1405006/71‑1 (MQ=255)
                                       aTCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTg                 <  1:3925919/70‑1 (MQ=255)
                                       aTCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTg                 <  1:2774602/70‑1 (MQ=255)
                                       aTCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTAcac                                        >  1:1418599/1‑45 (MQ=11)
                                        tCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaac                                 <  1:1805481/53‑1 (MQ=255)
                                        tCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTggg               <  1:4117580/71‑1 (MQ=255)
                                        tCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCGCa                     <  1:1763848/65‑1 (MQ=255)
                                        tCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTggg               <  1:3307673/71‑1 (MQ=255)
                                          ctctCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGca             <  1:953712/71‑1 (MQ=255)
                                            ctcAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGc                             <  1:2073144/53‑1 (MQ=255)
                                            ctcAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGcaca           >  1:1273358/1‑71 (MQ=255)
                                            ctcAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGcaca           >  1:1038134/1‑71 (MQ=255)
                                            ctcAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGcaca           >  1:2170482/1‑71 (MQ=255)
                                             tcAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACAt          >  1:3528298/1‑71 (MQ=255)
                                             tcAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACAt          >  1:2863005/1‑71 (MQ=255)
                                             tcAGACCAGCCAGGGATCGTCGCCTTGGTGAGCAGTTACCCCACCAACAAGCTAATCCCATc                   >  1:3715343/1‑62 (MQ=17)
                                              cAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATc         >  1:2700523/1‑71 (MQ=255)
                                              cAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATc         >  1:1088773/1‑71 (MQ=255)
                                               aGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACAt          <  1:704639/69‑1 (MQ=255)
                                               aGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACAt          <  1:3695249/69‑1 (MQ=255)
                                               aGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATcc        >  1:225837/1‑71 (MQ=255)
                                               aGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATcc        <  1:1713365/71‑1 (MQ=255)
                                               aGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATcc        <  1:1706176/71‑1 (MQ=255)
                                               aGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATcc        <  1:1531862/71‑1 (MQ=255)
                                                gACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCg       <  1:2056824/71‑1 (MQ=255)
                                                  ccagccagGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGAt     <  1:729254/71‑1 (MQ=255)
                                                  ccAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGAt     >  1:3637578/1‑71 (MQ=255)
                                                   cAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTaa                          <  1:747041/49‑1 (MQ=255)
                                                     gCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGc  <  1:2651394/71‑1 (MQ=255)
                                                     gCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGc  <  1:1195682/71‑1 (MQ=255)
                                                     gCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGc  <  1:1876723/71‑1 (MQ=255)
                                                      cTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTgg                <  1:2816326/56‑1 (MQ=255)
                                                      cTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGc  <  1:2681314/70‑1 (MQ=255)
                                                       |                                                                    
AGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGC  >  minE/1763501‑1763624

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