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
A22 F44 I0 R1 387 90.4 3244086 98.5% 3195424 139.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,018,983 A→T 20.9% intergenic (+46/+30) matP → / ← ompA Ter macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d)

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,018,9830AT20.9% 99.4 / 23.4 43intergenic (+46/+30)matP/ompATer macrodomain organizer matS‑binding protein/outer membrane protein A (3a;II*;G;d)
Reads supporting (aligned to +/- strand):  ref base A (21/13);  new base T (5/4);  total (26/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

AACGATTGTTCAGCTGATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGC  >  NC_000913/1018835‑1019131
                                                                                                                                                    |                                                                                                                                                     
aaCGATTGTTCAGCTGATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCgca                                                                                                                                                       <  1:102987/149‑1 (MQ=255)
        ttCAGCTGATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCagcagc                                                                                                                                                  <  2:713507/146‑1 (MQ=255)
        ttCAGCTGATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCagcagc                                                                                                                                                  >  1:713507/1‑146 (MQ=255)
          cAGCTGATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCTGCTGCGGGG‑t                                                                                                                                            <  3:535210/149‑1 (MQ=255)
          cAGCTGATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑t                                                                                                                                            <  1:634801/149‑1 (MQ=255)
            gCTGATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑ttt                                                                                                                                          <  4:37531/149‑1 (MQ=255)
               gATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTc                                                                                                                                       <  1:484523/149‑1 (MQ=255)
                   gAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTAcc                                                                                                                                   >  4:150158/1‑149 (MQ=255)
                     aGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAAACCCGCTGCTGCGGGG‑ttt                                                                                                                                          <  3:570968/140‑1 (MQ=255)
                     aGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAAACCCGCTGCTGCGGGG‑ttt                                                                                                                                          >  4:570968/1‑140 (MQ=255)
                                             cgcgAATAAAACGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAGGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGa                                                                                                         >  2:748030/1‑149 (MQ=255)
                                                 aaTAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCTGCTGCGGGG‑t                                                                                                                                            >  4:557118/1‑110 (MQ=255)
                                                 aaTAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCTGCTGCGGGG‑t                                                                                                                                            <  3:557118/110‑1 (MQ=255)
                                                            ttctCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTg                                                                                          >  3:451631/1‑149 (MQ=255)
                                                                ctGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATAc                                                                                      <  3:150158/149‑1 (MQ=255)
                                                                          aTCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTc                                                                            <  3:505292/149‑1 (MQ=255)
                                                                             tGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGAt                                                                         <  3:276696/149‑1 (MQ=255)
                                                                             tGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGAt                                                                         >  4:276696/1‑149 (MQ=255)
                                                                              gCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTaa                                                                                                                     <  4:183433/104‑1 (MQ=255)
                                                                              gCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTaa                                                                                                                     >  3:183433/1‑104 (MQ=255)
                                                                                    aTTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTAcg                                                                  >  2:715376/1‑149 (MQ=255)
                                                                                                 gAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAg                                                     >  1:513130/1‑149 (MQ=255)
                                                                                                   aTAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTaa                                                                                                                     >  3:555817/1‑83 (MQ=255)
                                                                                                   aTAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTaa                                                                                                                     <  4:555817/83‑1 (MQ=255)
                                                                                                   aTAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGcc                                                   <  1:748030/149‑1 (MQ=255)
                                                                                                                     ttCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTgca                                 >  1:364688/1‑149 (MQ=255)
                                                                                                                     ttCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTgca                                 >  3:132100/1‑149 (MQ=255)
                                                                                                                           ttACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGc                           <  2:364688/149‑1 (MQ=255)
                                                                                                                              cTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGt                        >  3:667603/1‑149 (MQ=255)
                                                                                                                              cTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGt                        >  2:691361/1‑149 (MQ=255)
                                                                                                                                 aaGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTc                     >  3:781742/1‑149 (MQ=255)
                                                                                                                                 aaGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAATCGATCAGTGCAGCACGCTATTTc                     <  1:691361/149‑1 (MQ=255)
                                                                                                                                    gCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACg                  >  3:96075/1‑149 (MQ=255)
                                                                                                                                      aaaaaaaaCCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGtt                >  1:738769/1‑149 (MQ=255)
                                                                                                                                        aaaaaaCCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGt              >  3:595410/1‑149 (MQ=255)
                                                                                                                                          aaaaCCCCGCTGCTGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCt                          <  4:19779/135‑1 (MQ=255)
                                                                                                                                          aaaaCCCCGCTGCTGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCt                          >  3:19779/1‑135 (MQ=255)
                                                                                                                                          aaaaCCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTca            <  4:595410/149‑1 (MQ=255)
                                                                                                                                           aaaCCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTcac           >  1:695658/1‑149 (MQ=255)
                                                                                                                                            aaCCCCGCTGCTGCGGGGTTTTTTTTGCCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTcac           >  2:309063/1‑149 (MQ=255)
                                                                                                                                            aaCCCCGCTGCTGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTcaca          >  2:616910/1‑149 (MQ=255)
                                                                                                                                            aaCCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTcaca          >  3:578912/1‑149 (MQ=255)
                                                                                                                                             aCCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCACTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAg         <  4:757484/149‑1 (MQ=255)
                                                                                                                                                ccGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAggcg      >  3:187018/1‑147 (MQ=255)
                                                                                                                                                ccGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGgtg      >  2:632634/1‑149 (MQ=255)
                                                                                                                                                 cGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGgtgt     >  2:528548/1‑149 (MQ=255)
                                                                                                                                                    agcagcGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGc  <  2:738769/149‑1 (MQ=255)
                                                                                                                                                    agcagcGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGCGTTGc  <  4:187018/149‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                     
AACGATTGTTCAGCTGATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAACCCCGCAGCAGCGGGG‑TTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGC  >  NC_000913/1018835‑1019131

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A