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
A11 F56 I1 R1 155 65.2 3164312 95.9% 3034575 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,728,444 C→A T33N (ACC→AAC)  rnt → RNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,728,4440CA98.5% 233.4 / ‑3.5 68T33N (ACC→AAC) rntRNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (36/31);  total (37/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.18e-01

TCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGAAC  >  NC_000913/1728350‑1728536
                                                                                              |                                                                                            
tCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGAt                                                                                          >  1:1309692/1‑99 (MQ=255)
tCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATg                                                                                         >  1:403754/1‑100 (MQ=255)
tCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATg                                                                                         <  1:1267415/100‑1 (MQ=255)
tCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATg                                                                                         >  2:614828/1‑100 (MQ=255)
 ccGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATgc                                                                                        >  2:219741/1‑100 (MQ=255)
   gATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATgcgc                                                                                      >  2:26167/1‑100 (MQ=255)
      aaCGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTCTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCgctgc                                                                                   <  2:902914/100‑1 (MQ=255)
       aCGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCgctgct                                                                                  <  1:846053/100‑1 (MQ=255)
       aCGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCgctgct                                                                                  >  1:1449654/1‑100 (MQ=255)
        cGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCtt                                                                                 >  2:216485/1‑100 (MQ=255)
        cGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGAGCGATGTTGAAACAGCCGGATTTAACGCCAAAAATGATGCGCTGCtt                                                                                 >  2:368695/1‑100 (MQ=255)
         gCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTg                                                                                <  2:551340/100‑1 (MQ=255)
         gCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTg                                                                                >  1:1382885/1‑100 (MQ=255)
         gCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTg                                                                                >  1:53571/1‑100 (MQ=255)
          cTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTga                                                                               <  1:626588/100‑1 (MQ=255)
              aCTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGAtt                                                                           >  1:764764/1‑100 (MQ=255)
                 tACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTgcc                                                                        <  2:508049/100‑1 (MQ=255)
                     ggTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCa                                                                    >  2:542480/1‑100 (MQ=255)
                     ggTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCa                                                                    >  2:399734/1‑100 (MQ=255)
                      gTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCAt                                                                   <  1:256993/100‑1 (MQ=255)
                        cTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCa                                                                 >  2:853044/1‑100 (MQ=255)
                            gCGACCGTTTTCGTGGTTTTTATCCTGGTGTTATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCAccc                                                              >  1:1275179/1‑99 (MQ=255)
                              gACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGa                                                           >  1:681180/1‑100 (MQ=255)
                                   ttttCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATg                                                      <  1:482999/100‑1 (MQ=255)
                                    tttCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATgg                                                     <  2:1330026/100‑1 (MQ=255)
                                     ttCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTCAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGa                                                    <  1:136464/100‑1 (MQ=255)
                                      tCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGAt                                                   <  1:767163/100‑1 (MQ=255)
                                       cGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATg                                                  <  2:495570/100‑1 (MQ=255)
                                       cGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATg                                                  >  1:754525/1‑100 (MQ=255)
                                          ggTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGatc                                               <  1:1071765/100‑3 (MQ=255)
                                          ggTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAAc                                               >  2:1114711/1‑100 (MQ=255)
                                          ggTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAAc                                               <  2:1275174/100‑1 (MQ=255)
                                           gTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACa                                              >  1:602757/1‑100 (MQ=255)
                                           gTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACa                                              <  2:134126/100‑1 (MQ=255)
                                            tttttATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTAGGATTGCAGCCATCACCCTGAAAATAGGTGaa                                                >  2:1207934/1‑97 (MQ=255)
                                               ttATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggc                                          >  2:759357/1‑100 (MQ=255)
                                               ttATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggc                                          <  2:1449646/100‑1 (MQ=255)
                                                tATCCTGTTGTTATCGATGTTGAAACAGCCGGATTTAACGCTAAAAACGCTGCGCTGCTTGAGATTGCCGCCATCACCATGAAGATTGATGAACAAagct                                         >  2:333714/1‑100 (MQ=255)
                                                tATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggct                                         <  1:216485/100‑1 (MQ=255)
                                                 aTCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctg                                        >  2:1269130/1‑100 (MQ=255)
                                                  tCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctgg                                       <  2:1307/100‑1 (MQ=255)
                                                   ccTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctggc                                      <  2:681178/100‑1 (MQ=255)
                                                    cTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctggct                                     <  1:26167/100‑1 (MQ=255)
                                                    cTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctggct                                     >  2:772824/1‑100 (MQ=255)
                                                    cTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctggct                                     <  2:175997/100‑1 (MQ=255)
                                                       ttgtGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGAt                                  >  2:107718/1‑100 (MQ=255)
                                                           gATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCg                              >  2:269391/1‑100 (MQ=255)
                                                           gATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCg                              >  2:1566625/1‑100 (MQ=255)
                                                           gATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCg                              >  1:515907/1‑100 (MQ=255)
                                                           gATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCg                              >  2:657787/1‑100 (MQ=255)
                                                            aTCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCgg                             <  1:594472/100‑1 (MQ=255)
                                                              cGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGac                           <  2:1391383/100‑1 (MQ=255)
                                                               gATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGaca                          <  1:1551197/100‑1 (MQ=255)
                                                                  gTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCTCCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGAcacca                       >  2:1107088/1‑100 (MQ=255)
                                                                   ttGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGAcaccac                      <  2:1324530/100‑1 (MQ=255)
                                                                    tGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCCTGTGATTGTCGCCATCACCCTGAAAATTGATGAACAAGGCTGGCTGATGCCTGAcaccac                      <  2:1113323/99‑1 (MQ=255)
                                                                     gAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCacat                    >  2:573822/1‑100 (MQ=255)
                                                                        aCAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCacattac                 <  1:1443672/100‑1 (MQ=255)
                                                                         cAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCacattaca                <  2:1352559/100‑1 (MQ=255)
                                                                            ccGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCacattacatt              >  1:1008426/1‑99 (MQ=255)
                                                                              ggATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTcc           <  1:746251/100‑1 (MQ=255)
                                                                                  ttAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGt       >  1:1467737/1‑100 (MQ=255)
                                                                                   tAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTc      >  2:1376291/1‑100 (MQ=255)
                                                                                   tAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTc      <  2:905308/100‑1 (MQ=255)
                                                                                    aaCGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCg     >  1:109139/1‑100 (MQ=255)
                                                                                    aaCGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCg     >  1:108560/1‑100 (MQ=255)
                                                                                      cGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGaa   >  1:1289338/1‑100 (MQ=255)
                                                                                       gCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGAAc  <  2:703932/100‑1 (MQ=255)
                                                                                              |                                                                                            
TCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGAAC  >  NC_000913/1728350‑1728536

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A