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
A6 F17 I0 R1 29 52.5 1051376 97.9% 1029297 229.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,206,438 G→A 30.6% intergenic (‑182/‑25) ttdR ← / → ttdA transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,206,4380GA30.6% 38.3 / 5.8 31intergenic (‑182/‑25)ttdR/ttdAtranscriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base G (6/14);  new base A (3/6);  total (11/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAG‑ACAAATACAAAAACTGGAGTTGCCATGATGA‑GCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTA‑CCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAA  >  NC_000913/3206219‑3206647
                                                                                                                                                                                                                           |                                                                                                                                                                                                                    
aCCAGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGGATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAG‑ACAAATACAAAAACTgg                                                                                                                                                                                                    <  1:103623/237‑1 (MQ=255)
                cTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAG‑ACAAATACAAAAACTGGAGTTGCCATGATGA‑GCg                                                                                                                                                                                  <  2:269075/238‑1 (MQ=255)
                    aGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCACTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCTCGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAG‑ACAAATACAAAAGCTGGAGTTGCCATGATGA‑GCGAAAGt                                                                                                                                                                             <  1:51212/239‑1 (MQ=255)
                             aTTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAG‑ACAAATACAAAAACTGGAGTTGCCATGATGA‑GCGAAAGTAATAAGCaa                                                                                                                                                                    <  1:285995/239‑1 (MQ=255)
                              ttCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGGAATTTTTCAC‑AAAAAAACAAAAAATGGAGTTGTCCTTGTGT‑GGGAAAGTAATAAGAAAc                                                                                                                                                                   >  2:250348/1‑239 (MQ=255)
                               tCAGCATCGTTAATTATCCGCAGTTTTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCTTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAG‑ACAAATACAAAAACTGGAGTTGCCATGATGA‑GCGAAAGTAATAAGCAACa                                                                                                                                                                  <  2:341723/239‑1 (MQ=255)
                                   cATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTTAT‑ACCAAAAAAAAAAATCGAGTTGGCCTGATTA‑GCGACAGGAATAAACaaacagca                                                                                                                                                              >  2:25988/1‑233 (MQ=255)
                                    aTCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAG‑ACAAATACAAAAACTGGAGTTGCCATGATGA‑GCGAAAGTAATAAGCAACAGGc                                                                                                                                                               <  1:195128/237‑1 (MQ=255)
                                        ttAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGAGAATTTTTTCAG‑ACAAAAAAAAAAAATTGAGTTTCCATGGTGA‑GCGAAAGGAATAAGAAAAAGGCAATGaa                                                                                                                                                         >  1:103531/1‑239 (MQ=255)
                                                              aGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTTAA‑ACAAAAACAAAAAAAGTAGTTGCCATGATGA‑GCGGAAGTAATAAACAACAAGCAGTGAATAAGATTACAGAGATTTTAGCt                                                                                                                                   >  1:13288/1‑239 (MQ=255)
                                                                               aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCTGAAAAAATAC‑AAAACAGGAGATGTCATGTAGAGGGGAAATAAAAAAAAAACAGGAAGAGAAAAGATTAACA‑AGATTGTTGCTACATTTAACACCATggt                                                                                                                  >  1:389349/1‑237 (MQ=255)
                                                                                 aaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCCA‑CCAAAAAAAAAAACTGTAGATGGCGTTTAGA‑GGGAAAGTAATAAACAACAAGAACTGAATAAATTGATAGAGAGTGTTAGCAACTTTACCGCCCTGAatt                                                                                                                >  2:54487/1‑239 (MQ=255)
                                                                                   ctttGCCTTTCCCTGCTCTGGCGAAATATTCATTCTTATTTTCGTGTTAATTCACAAACTGTTAATTAAATATTCAGGGTGGCAAAAAATAAAAAACCACATTTTTAGTGGTAGTTTGGGGGGGTGAATTTTTCCAA‑AAAAATACAAAAACTGGAGTGGCCATGATGA‑GCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCt                                                                                                              <  2:13288/237‑1 (MQ=255)
                                                                                         cATTCCCCGCTCGGGCGAAATATTCATTCTTATTTTCGTGTTGATTCACGAACTGTTAATTAAATATTCACGGTGGAAAAAAATATAAAACCACATTTTTAGGGGTAGTTGGTGGGGGTGAATTTTTCAAG‑ACAAATAAAAAAACTGGGTTTGCCATGATGA‑GCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTGGTTAACTTTACCGCCATGATTTCTA‑CCCGa                                                                                                       <  2:389349/239‑1 (MQ=255)
                                                                                          aTTCCCTGCTCTGGCTAAATTTTAATTCTTTTTTCCGCGTTATTTCACGAACTGTTAATTACATATTCGCGGTGGCAAAAAATATAAAACCACATTTTTATGGGTAGTTTGTGGGGGTAAATTTTTCCAG‑ACAAATACAAAAACTGGAGTTGCCATGATGA‑GCGAAAGTAATAAGCAACAGGCAGTAAATAAGTTGACAGAGATTGTCGTTAACTTTACCGCCATGATTTCTA‑CCCGaa                                                                                                      <  2:210357/239‑1 (MQ=255)
                                                                                                tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGGAAATTTTCAG‑ACAAATAAAAAAAATTGAATTGCCATGGTGA‑GGGGAAGTAATAAGCAAAACGCAGTGAATAAATTTGCAGAGATTGTTGCTAACATTACCGGCCTGATTTTTATCCCGatagctg                                                                                                 >  1:435241/1‑233 (MQ=255)
                                                                                                      ggCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGAGAGATTTTTTAG‑ACAAAAACAAAAACAAGAGTTGCGATGGTGA‑GCGCAAGTAATAAACAAAAGAGAGGGAATAAATTGACAGAGAATTTTGCTCACTTTACCGCCACGATTTTTT‑ACCGCAAGCCtgtttatg                                                                                          >  1:150395/1‑233 (MQ=255)
                                                                                                       gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGGATTTTTTTAG‑AAAAAAAAAAAAAATGGAGTTTGCATGAGTA‑GGGGAAGGTATAAACAAAAAGCAAGGAAAAAAGTTACAGAGATTGTCGCTAAATTTACACCCCTGATTTTCA‑ACCGAAAGCCtggttgaat                                                                                         >  2:57195/1‑232 (MQ=255)
                                                                                                         gcAATATTCATTTTTATTTTCGCTTTGATTAACAAACTGTTAATTATATATTCTGGGTGGCAAAAAATATAAAACCACATTTTGAGTGGTAGTTTGGGGCGGTGAATTTTTCAAG‑AAAAATAAAAAAACTGGAGTTGCCATGATGA‑GCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTA‑CCCGAATGCCTGATGACgtg                                                                                        <  2:435241/238‑1 (MQ=255)
                                                                                                             tatTCATTCTTATTTTGGCGTTAATTCACAAACTGTTAATTACATATTGAGGGTGGAAAAAAATATAAACCCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTACCAG‑AAAAATACAAAAACTGGAGTTGCCAGGATGA‑GCGAAATTAATAAGCAACAGGCAGAGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTA‑CCCGAATGCCTGATGACGTGGTGGa                                                                                   <  1:25988/239‑1 (MQ=255)
                                                                                                             tatTCATTCTTATTTACGCGTTGATACACGAACTTTTAATTACATTTTCCCGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAG‑ACAAATACAAAAACTGGAGTTGCCATGATGA‑GCGAAAGTAATAAGCAACAGGCAGTAAATAAGTTGACAGAGATTGTCGCTACCTTTCCCGCCATGATTTCTA‑CCCGAATGCCTGATGACGTGGTGGa                                                                                   <  2:266158/239‑1 (MQ=255)
                                                                                                                          tttCGCTTTAATTCGAGAACTTTTAATTACATATTCACGGTGGCAAAAAATAAAAACCCACATTTTTAGTGGTATTTTGTGGCGGTGAATTTTTCAAA‑AAAAATAAAAAAACTGGATTTGCCATGATGA‑GCAAAAGTAATAACCAACGGGCAGTAAATAATTTGACAGAAATTGTCGCTAACTTTACCGCCATGATTTCTA‑CCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAg                                                                      <  1:12985/239‑1 (MQ=255)
                                                                                                                                                tgaaTTACATATTCACGGTGGAAAAAATAATAAACACCCATTTTAATTGGTATTTTGGTGGGGTTAATTTTCCAAA‑ACAAATAAAAAAACTGGAGTTGCCATGAGGA‑GCTAATGTATTAAGAAACAGGCAGTAAAAAATTTGACAGAGATTGTCGTGAACTTTACCGCCATGATTTCTA‑CCCGAATGCCTGATGACGTGGTGGATAAACTaaaa                                                                         <  1:363901/212‑1 (MQ=255)
                                                                                                                                                         tatTCAGGTGGGAAAAAAATAAAAAACCACATTTTTAGTGGTAGTTTGGGGCGGTGAATTTTTCCAG‑AAAAATACAAAAACTGGAGTTGCCATGATGA‑GCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTAACCGCCATGATTTCTA‑CCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGa                                       <  2:103531/239‑1 (MQ=255)
                                                                                                                                                         tatTCACGGTGGCAAAAAAAAAAAACCCACATTTTGAGTGGTAGTTTGTGGCGGTGAATTTTCCCAA‑CAAAAAACAAAAACTGGGGTTGCCATGATAA‑GCAAAATTAATAAGCAACAGACAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTA‑CCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGa                                       <  1:287084/239‑1 (MQ=255)
                                                                                                                                                          atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAA‑AGAAAAACAAAAAAACGAGGTTTCATGTTGA‑GCGAAAGTAAAAAACAACACGAAGTGAATAAGATGTCAGAGACTTTCGCTAACATTATCACCAAGATTTCTA‑TCCCAAAGTCTGATAACGTTGTGGTGAAACTAAAACAGATaaaag                                                               >  1:99391/1‑212 (MQ=255)
                                                                                                                                                                 ggagaaaaaaaTAAAAAACCATATTTTTAGGGGTAGTTTGGGGCGGTAAATTTTTCCAA‑AAAAATAAAAAAACTGGAGTTGACATGATGA‑GCAAAAGAAATAAGCAACAGGAAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTA‑CCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTAt                                <  2:219371/233‑1 (MQ=255)
                                                                                                                                                                  tGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAG‑ACAAAAACAAAAAAATGAGGTGGCATGATGA‑GGGGAAGGAATAAAAAAAAAGCAAAGAAAAAATTGAAAGAGAATGTTGCTAAATTTTACGCCATGATTTTTA‑CCCCAAAGCCTGATGACGTGGGGGATAAACTAAAAAAGCTAAAAGATGCCGGAACGACGTCGATTGGGGAAATTATCt                              >  1:170046/1‑239 (MQ=255)
                                                                                                                                                                          aaTAAAAACCAACATTTTTAGTGGTATTTTGGGGGGGTAAATTTTCCCAA‑AAAAATACAAAAACGGGAGTTGCCATGAGGA‑GCGAAAGAAAAAAACAACAGCCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTAGCCGCCATGATTTCTA‑CCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACg                      <  1:92411/239‑1 (MQ=255)
                                                                                                                                                                            taaaaaaCCAAATTTTTAGTGGTAGTTTGGGGGGGTGAATTTTTCAAG‑AAAAATAAAAAAACGGGAGTTGCCAGGATGA‑GCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTA‑CCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGa                                       <  2:187751/217‑1 (MQ=255)
                                                                                                                                                                                               gggTAGTTGGGGGCGGTGAATTTTTCAAG‑AAAAAAAGAAAAACTGGAGTGGCCATAATGA‑GAAAAAGTAATAAGAAACGGGCAGTGAATAAGTTGAAAGGGATTGTGACTAATTGTACCGCCATGATTTCTA‑CCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCaaaa  <  1:250348/237‑1 (MQ=255)
                                                                                                                                                                                                                           |                                                                                                                                                                                                                    
ACCTGCAAGTCTTTGGCTAAAGGCCAGCTATTCAGCATCGTTAATTATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAG‑ACAAATACAAAAACTGGAGTTGCCATGATGA‑GCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTA‑CCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAAAGGATGCCGAAACGTCGTCGATGGGGAAAATTATCTACCATACGATGTTCGACAACATGCAAAA  >  NC_000913/3206219‑3206647

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A