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 F212 I1 R1 174 80.0 3892211 96.7% 3763768 99.9

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_0009131,728,4440CA95.2% 210.4 / 2.6 62T33N (ACC→AAC) rntRNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair
Reads supporting (aligned to +/- strand):  ref base C (1/2);  new base A (30/29);  total (31/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

CGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGAACCATT  >  NC_000913/1728352‑1728540
                                                                                            |                                                                                                
cGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATgcg                                                                                           >  1:228201/1‑100 (MQ=255)
 gATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATgcgc                                                                                          <  2:438226/100‑1 (MQ=255)
   tAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCgctg                                                                                        >  1:649624/1‑100 (MQ=255)
    aaCGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCgctgc                                                                                       >  1:41462/1‑100 (MQ=255)
    aaCGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCgctgc                                                                                       <  2:154029/100‑1 (MQ=255)
      cGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCtt                                                                                     >  1:1149242/1‑100 (MQ=255)
       gCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTg                                                                                    <  1:542366/100‑1 (MQ=255)
       gCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTg                                                                                    >  2:462144/1‑100 (MQ=255)
       gCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATACTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTg                                                                                    >  1:1543130/1‑100 (MQ=255)
        cTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTga                                                                                   <  2:830044/100‑1 (MQ=255)
        cTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTga                                                                                   >  1:1719868/1‑100 (MQ=255)
         tCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTgag                                                                                  <  1:1107227/100‑1 (MQ=255)
         tCAACTTACCGGTCTGTGCGACCGTTTTCGTGGGTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTgag                                                                                  >  2:1030824/1‑100 (MQ=255)
          cAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTgaga                                                                                 >  1:524727/1‑100 (MQ=255)
          cAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTgaga                                                                                 >  2:1528603/1‑100 (MQ=255)
          cAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTgaga                                                                                 <  2:193708/100‑1 (MQ=255)
               tACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTgcc                                                                            >  2:880190/1‑100 (MQ=255)
                aCCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTgccg                                                                           <  1:868576/100‑1 (MQ=255)
                  cGGTCTGTGCGACCGTTTTCGTGGTTTTGATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTgccgcc                                                                         <  1:186445/100‑1 (MQ=255)
                     tCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATc                                                                      >  2:1725020/1‑100 (MQ=255)
                       tgtgCGACCGTTTTCGTGGTTTTTATTTTGTTTTGATGGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCTCCATCAc                                                                    >  1:1046747/1‑100 (MQ=255)
                       tgtgCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCAc                                                                    <  2:1163278/100‑1 (MQ=255)
                        gtgCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCAcc                                                                   >  2:1053267/1‑100 (MQ=255)
                         tgCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCAccc                                                                  >  2:839621/1‑100 (MQ=255)
                              ccGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGATGCTTGAGATTGCCGCCATCACCCTGaaa                                                             >  1:529074/1‑100 (MQ=255)
                                 ttttCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACTATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATg                                                          <  1:1662046/100‑1 (MQ=255)
                                 ttttCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATg                                                          <  1:294937/100‑1 (MQ=255)
                                    tCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGAt                                                       <  2:1506920/100‑1 (MQ=255)
                                     cGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATg                                                      <  2:674805/100‑1 (MQ=255)
                                     cGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATg                                                      <  2:1786385/100‑1 (MQ=255)
                                       tGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGaa                                                    >  2:1276323/1‑100 (MQ=255)
                                         gTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACa                                                  <  1:1312482/100‑1 (MQ=255)
                                                 ccTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctggc                                          >  1:213065/1‑100 (MQ=255)
                                                 ccTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctggc                                          <  1:95986/100‑1 (MQ=255)
                                                 ccTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctggc                                          <  2:1719879/100‑1 (MQ=255)
                                                  cTGTTGTGATCGATGTTGAAACAGCCTGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctggct                                         <  1:1790418/100‑1 (MQ=255)
                                                  cTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAggctggct                                         <  1:977650/100‑1 (MQ=255)
                                                    gttgtGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGa                                       <  1:308011/100‑1 (MQ=255)
                                                     ttgtGATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGAt                                      <  1:462142/100‑1 (MQ=255)
                                                         gATCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCg                                  <  2:1501069/100‑1 (MQ=255)
                                                          aTCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGGTGAACAAGGCTGGCTGATGCCgg                                 >  1:1400637/1‑100 (MQ=255)
                                                          aTCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCgg                                 >  1:676645/1‑100 (MQ=255)
                                                          aTCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCgg                                 <  2:26606/100‑1 (MQ=255)
                                                           tCGATGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGa                                >  1:1829987/1‑100 (MQ=255)
                                                               tGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGAcacc                            >  1:37593/1‑100 (MQ=255)
                                                               tGTTGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGAcacc                            <  1:1613153/100‑1 (MQ=255)
                                                                 ttGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGAcaccac                          >  2:1379585/1‑100 (MQ=255)
                                                                  tGAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACcaca                         >  2:332461/1‑100 (MQ=255)
                                                                   gAAACAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCacat                        >  2:299970/1‑100 (MQ=255)
                                                                      aCAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCTGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCacattac                     <  2:1753602/100‑1 (MQ=255)
                                                                       cAGCCGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCacattaca                    >  1:840156/1‑100 (MQ=255)
                                                                          ccGGATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACAttt                 >  2:1207858/1‑100 (MQ=255)
                                                                            ggATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTcc               >  1:1385796/1‑100 (MQ=255)
                                                                            ggATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTcc               <  1:1527362/100‑1 (MQ=255)
                                                                             gATTTAACGTCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCa              <  1:1484690/100‑1 (MQ=255)
                                                                             gATTTAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTAATGCCGGACACCACATTACATTTCCa              <  1:1331766/100‑1 (MQ=255)
                                                                                ttAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGt           <  1:1548707/100‑1 (MQ=255)
                                                                                 tAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTc          >  2:184930/1‑100 (MQ=255)
                                                                                 tAACGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTc          >  2:390941/1‑100 (MQ=255)
                                                                                    cGCCAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGaa       <  2:1258868/100‑1 (MQ=255)
                                                                                     gCCAAAAACGATGCGCTTCTTGAGATTGCCGCCAGCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGa        <  1:1766620/98‑1 (MQ=255)
                                                                                       cAAAAACGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGAACCa    >  1:319666/1‑100 (MQ=255)
                                                                                         aaaaCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGAACCAtt  <  1:1590810/100‑1 (MQ=255)
                                                                                            |                                                                                                
CGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGAACCATT  >  NC_000913/1728352‑1728540

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A