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
A3 F9 I0 R1 74 77.5 1840812 85.2% 1568371 224.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,206,506 C→A 26.1% T15K (ACA→AAA)  ttdA → L‑tartrate dehydratase, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,206,5060CA26.1% 65.0 / 3.1 33T15K (ACA→AAA) ttdAL‑tartrate dehydratase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (15/9);  new base A (2/7);  total (17/16)
Fisher's exact test for biased strand distribution p-value = 5.70e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

CGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACA‑TTTTTAGTG‑G‑TAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCC‑ATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTCCTGCCTGTCAGGACACCGGGGAGATTATGTTCTTCGTTAAAGTCGGTTCCCGCTTCCCACTGCTTGGCGAGCTGCAA  >  NC_000913/3206283‑3206744
                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                              
cgcAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACA‑TTTTTAGTG‑G‑TAGTTTGTGGCGGTGAATTTTTCCAATCAAATACAAAAAAAAGAGTTTCC‑ATGGTGAGG‑GCAAGAAATAAACAACAAGAAGTGGATAAAATGAAAGAGAATGTCTCTaa                                                                                                                                                                                                                                 >  1:485897/1‑239 (MQ=255)
                             cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACA‑TTTTTAGTG‑G‑TAGTTTGTGGCGGTGAATTTTTTCCGACAAAAACAAAAAATGGAGGTGGC‑CTGATTAGG‑GAAAGGAATAAACAAAAGGCAGAGGATAAATTGCAAGAGATTTTCGCTAACTTTTCCGCCCTGAtttttcaccgcaag                                                                                                                                                                                                     >  1:200125/1‑227 (MQ=255)
                                        cgaataattcattcTTTTTTACGCGTTGATGCACACACTTTTATTTACATAGTAACGGTGGAAAAAATAATAAACCCATA‑TTTTAAGTG‑A‑TATTTTGGGGCGGTAATTTTTTCTAGACAAATAAAAAAACGGAAGTTGCC‑ATGATGGTC‑AAAATTAATAAGCAACAGGAAGTAAATAGTTTGACAGATATTGTCGCTACTTTAACCGCCATGATTTCTACCCGAATGCCTGATGACgt                                                                                                                                                                                          <  1:773826/232‑1 (MQ=255)
                                                       tATTTTGGTGTTGATTCACGAACTGTTAATTACATTTTCACGGGGGAAAAAAATATAAACCCAAA‑TTTTTGGGG‑G‑TAGTTGGGGGCGGTGAATTTTCCCAGAAAAATAAAAAAACTGGAGTTGCC‑ATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaaaa                                                                                                                                                                          <  1:729240/239‑1 (MQ=255)
                                                                                         tatTCGCGGGTGAAAAAAACA‑AAAACCATA‑TTTTTGATG‑GTTAGTTGTGGGCGGGGAATTTCTCAAAACAAAAACAAAACGTGGA‑TTGCCAAGGATGAGC‑AAAATTAAAAAGCAACGGGAAGTAAATAAGTGGACAGAGTTTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGa                                                                                                                                        <  1:646094/239‑1 (MQ=255)
                                                                                                gggtaaaaaaaaaaaaaaaaCAAA‑TTTTGGGTG‑G‑TTTGTTGGGGGGTAGAATTTTTCAAGAAAAATCAAAAAAGTGAGGTGGCC‑ATGTGGAGG‑AAAATAAATAACAAACGGGTAGTGAATAGGTGAAAGGAGATTGTCGTTAATTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTAt                                                                                                                                 <  2:752705/233‑1 (MQ=255)
                                                                                                ggggaaaaaaaaTA‑AAAACCCCAGTTTTGAGTG‑G‑GTGTTTGGGGCGGGGAATTTTTCCAGCAAAATAAAAAACCTGGAGTTGCC‑AGGATGATC‑GAAATAAACAACCAGCAGTCTGTAAATAATTTGACAGAGTTTGTCGCTACCTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTAt                                                                                                                                 <  1:134800/233‑1 (MQ=255)
                                                                                                 ggtggaaaaaaTTAAAAACCAAA‑TTTTTATTGTG‑TAGGTTGTGGGGTTAATTTTTTCGAAGAAAAGAAAAAAACTGAAATTTCC‑ATGAAGTGC‑GAAATTAAAAGGAAATATGGAGTGAAAAAGTTGAAAGAGTTTGTCCTCACCTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTAt                                                                                                                                 <  1:363412/234‑1 (MQ=255)
                                                                                                 gTGGAAAAAAATAAAAAACCAAT‑TTTTTAGTG‑G‑TAGTTTGGGGCGGTAAATTTTACCAGAAAAATAAAAAAACTGGGTTTGCC‑ATGATGAGA‑GAAAGTAATAAGCAACAGGCAGTAAATAAGTTGAAAGAGATTGTCGCTAATTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTAt                                                                                                                                 <  1:577720/238‑1 (MQ=255)
                                                                                                          ataataAAACCAAT‑TTTTTAGTG‑G‑GATTTGGGGGGGGGAAATTTTTCAAAAAAAGAAAAAAAACTGGAGTGGCA‑ATGAGGAGA‑AAAAGTAATAAGCAACTGGAAGTGAATAAGTTGAAAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACg                                                                                                                       <  2:284148/236‑1 (MQ=255)
                                                                                                                        ttttttAGTG‑G‑TAGTTGGGGGGGGTAAATTTTCCCAGACAAAAACAAAAACTGGATTTGCC‑ATGAGGAGC‑GAAAGTAATAACCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGacaaca                                                                                                          <  1:919112/238‑1 (MQ=255)
                                                                                                                                 g‑g‑TAGTTTGTGGCGGTGAATTTTTCCAGAAAAATACAAAAACTGGAGTTGCC‑ATGATGAGC‑AAAAGTAATAAGCAAAAGGCAGTGAATAAGTTAGAAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCaaaa                                                                                                   <  1:605525/237‑1 (MQ=255)
                                                                                                                                      aGTTGGGGGGGGTAAATTTTTCCAGACAAATAAAAAAAGTGGAGGTGCC‑GTTATGGGC‑AAACGTAACAAGCAACAGGCAGTGAATAAGTTGACAGAGTTTGCCGCTATCTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa                                                                                              <  1:164983/239‑1 (MQ=255)
                                                                                                                                       gTTGGTGGGCGTGAATTTTACAAAAAAAATACAAAAACGGGAGGTG‑C‑AAGAGGAGCGGAAATTAAAAAGCAACGGGCACGAAATAGTTGGACGGAGATTGGCGCAACCTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGa                                                                                              <  1:733821/238‑1 (MQ=255)
                                                                                                                                                                   aTACAAAAACTGGAGTTGCC‑ATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGCGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGTTGGGGAAAATTATCTTCCATACGATTTTCGACAACATCCAAAAAGCGATTAGCCTGAATCGTCCTGCCTTACAGGa                                                                  >  1:862013/1‑238 (MQ=255)
                                                                                                                                                                   aTACAAAAACTGGAGTTGCC‑ATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGACTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACGACATGCAAAAACCGATTGACCTGAATCGCCCTGCCTGCCAgaa                                                                  >  1:879339/1‑236 (MQ=255)
                                                                                                                                                                          aaCGGGAGTTGCC‑ATGAGGAGC‑AAAATTAAAAAGAAAAGGGCATTGAATAGGTGGAAAGGGTTTGTCGTTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTCCTGCCTGTCAGGACACCgggg                                                          <  1:840587/239‑1 (MQ=255)
                                                                                                                                                                               gAGTTGCC‑ATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTCCTGCCTGTCAGGACACCGGGGAGAtt                                                     >  1:10664/1‑239 (MQ=255)
                                                                                                                                                                                                c‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACg                                                                                                                       >  1:551746/1‑157 (MQ=255)
                                                                                                                                                                                                c‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAAAAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTCCGACAACATGCAAAAACCGATTGACCTGAATCGACCTGCCTGTCGGAAAAACGGGGAGATTAAGTTTTTCGTaaaaa                                     >  2:460051/1‑238 (MQ=255)
                                                                                                                                                                                                   aaaGAAATCAGAAACGGGCAGGAAAAAGGTTGCCAGATGTTTTCGTAATATTTACCGCCATGATTTATACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTCCTGCCTGTCAGGACACCGGGGAGATTATGTTCTTCGTTAAAGt                                    <  1:671095/238‑1 (MQ=255)
                                                                                                                                                                                                        aaaacgCAACAGGCAGTTAAAATGTTAAAAGATATTGGCCATAATTTCACCGCCATTATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTCCTGCCTGTCAGGACACCGGGGAGATTATGTTCTTCGTTAAAGTCGGTTc                              <  1:199503/234‑1 (MQ=255)
                                                                                                                                                                                                                 cAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTCCTGCCTGTCAGGACACCGGGGAGATTATGTTCTTCGTTAAATTCGGTTCCCGCTTcc                      >  1:724414/1‑238 (MQ=255)
                                                                                                                                                                                                                    gCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTCCTGCCTGTCAGGACACCGGGGAGATTATGTTCTTCGTTAAAGTCGGTTCCCGCTTCCCAc                   >  1:178404/1‑238 (MQ=255)
                                                                                                                                                                                                                      aGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGCTTGACCTGAATCGTCCTGCCTGTCAGGCACCCGGGGAGATTATTTTCTTCGTTAAAGTCGGTTCCGCCTTCCCACTGc                >  2:38329/1‑239 (MQ=255)
                                                                                                                                                                                                                        tGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTCAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATTTTCGACACCATGCAAAAAGCGATTGACCTGAATCGTCCGGCCTGTCAGGCCACCGGGGGGTTTACGTTCTCTGTTAAAACCGGTTCACGGTTcccccctctt              >  2:730345/1‑232 (MQ=255)
                                                                                                                                                                                                                        tGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCAATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCATCCTGCCTGTCAGGACACGGGGGAGATTATGTGTTGCGTTAAAGTCGGTTCCCGCTTccaccggctt              >  1:693775/1‑231 (MQ=255)
                                                                                                                                                                                                                                  gACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTcctgcc                                                                          >  1:258738/1‑169 (MQ=255)
                                                                                                                                                                                                                                  gACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTcctgcc                                                                          <  2:258738/169‑1 (MQ=255)
                                                                                                                                                                                                                                  gACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTCCTGCCTTTCGGGAAACCGGGGAGATTATTTTATTCGTTAAAAGCGGTTCCCGCTTCCCACTGCTTgcgaatctga    >  2:309504/1‑230 (MQ=255)
                                                                                                                                                                                                                                  gACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTCCTGCCTGTCAGGACACCGGGGAGATTATGTTTTTCGTTAAAGTCGGTTCCCCCTTCCCACTGCTTgcgggctcgc    >  2:755432/1‑230 (MQ=255)
                                                                                                                                                                                                                                  gACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTCCTGCCTGTCAGGACACCGGGGAGATTATGTTCTTCGTTAAAGTCGGTTCCCGCTTCCCCCTGCTTGGCGAGCTGc    >  1:625242/1‑239 (MQ=255)
                                                                                                                                                                                                                                  gACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTCCTGCCTGTCAGGACACCGGGGAGATTATGTTCTTCGTTAAAGTCGGTTCCCGCTTCCCACTCCTTGGGCAGCTGc    >  1:106703/1‑239 (MQ=255)
                                                                                                                                                                                                                                    cAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATCAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTCCTGCCTGTCAGGACACCGGGGAGATTATGTTCTTCGTTAAAGTCGGTTCCCGCTTCCCACTGCTTGGCGAGCTGCaa  >  1:242875/1‑239 (MQ=255)
                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                              
CGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACA‑TTTTTAGTG‑G‑TAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCC‑ATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAAAGCGATTGACCTGAATCGTCCTGCCTGTCAGGACACCGGGGAGATTATGTTCTTCGTTAAAGTCGGTTCCCGCTTCCCACTGCTTGGCGAGCTGCAA  >  NC_000913/3206283‑3206744

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A