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
A14 F19 I0 R1 34 56.7 1876034 94.8% 1778480 147.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913_3_pae_tpiA 2,679,525 G→T 100% A1074D (GCT→GAT)  yphG ← DUF4380 domain‑containing TPR repeat protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA2,679,5250GT100.0% 139.0 / NA 47A1074D (GCT→GAT) yphGDUF4380 domain‑containing TPR repeat protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (22/25);  total (22/25)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AGGGTTTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCAGGTTG  >  NC_000913_3_pae_tpiA/2679380‑2679670
                                                                                                                                                 |                                                                                                                                                 
aaggcttttATCAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTTATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATTAGGGTGGTGAATAATGCCGCTTTTGGCCAATCCg                                                                                                                                                <  1:327106/144‑1 (MQ=255)
        tattaACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGCGGAGGGGCGCTTTCGGCCAATCCGGATTAATc                                                                                                                                        <  2:667577/149‑1 (MQ=255)
         attaACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCg                                                                                                                                       >  2:301741/1‑149 (MQ=255)
                acGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCaa                                                                                                                                <  1:902479/149‑1 (MQ=255)
                  ggattattaTAATTATTTTGTGATGAGCAGATGCGCGTGCCGCTCAAATATTAAAGTTAATAGGGTTTAGTGTATGCGGTTAAAAATAAAAGGCATCACGGTGGTCAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAAtt                                                                                                                              <  2:69222/146‑1 (MQ=255)
                  ggCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAAtt                                                                                                                              <  1:567334/149‑1 (MQ=255)
                   gCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTc                                                                                                                             >  1:790080/1‑149 (MQ=255)
                   gCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTc                                                                                                                             >  1:292844/1‑149 (MQ=255)
                         tCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGGTTAGTGAACGCGGTTAAAAATAAAAGGAATCAGGGTGGTGAATAATGCCTCTTTTGGACAATTACGAGTTATCGCCGTCAATTCcgcgtg                                                                                                                       >  2:892850/1‑147 (MQ=255)
                             attattTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCa                                                                                                                   <  1:901987/149‑1 (MQ=255)
                                  tttGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTc                                                                                                              <  2:497980/149‑1 (MQ=255)
                                     gtgATGAGCGGCAGCCCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCCTCACGGTGGTGAATAATGCCGCTGTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCata                                                                                                           <  1:650701/149‑1 (MQ=255)
                                      tgatgaGCGGCAGCGCGTGCAGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACAGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGACGTCAATTCAGCTCGAACAGACtgcaat                                                                                                          >  2:267408/1‑144 (MQ=255)
                                       gatgaGCGGCAGCGCGTGCCGCTCAAATAATACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGCNACTTCAGCGCGAGCAGACTCACAtt                                                                                                         >  1:615085/1‑149 (MQ=255)
                                             cGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCaa                                                                                                   <  1:793714/149‑1 (MQ=255)
                                              gggaGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAAc                                                                                                  <  1:301084/146‑1 (MQ=255)
                                                     tgTGCCGCTCAAAGATTACAGTTAATAGGGTTTAGTGACCGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTTATATTGCGCAACCTCCCCg                                                                                           <  2:346382/148‑1 (MQ=255)
                                                             tCAAATATTACAGTCAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCcgc                                                                                   <  1:16155/149‑1 (MQ=255)
                                                                         gTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCAt                                                                       <  1:878966/149‑1 (MQ=255)
                                                                          ttgagaGGGTTTAGTGAACGGGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATc                                                                      <  1:5740/144‑1 (MQ=255)
                                                                            aaTAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGc                                                                    <  1:141323/149‑1 (MQ=255)
                                                                            aaTAGGATTTAGTGAGCTCTGTTAAAAATAAAAGGCATCGCGGTGGTGATTAATGCCGCTTTCGGCCAATTCGGATTATTTGCCGATAATTCAACGCGCGCGGTCTCATATTGCGCAACCTCTCTGTGTCTCGCGGACGCTAGCATCGc                                                                    <  2:428799/149‑1 (MQ=255)
                                                                                 ggTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGccacca                                                               >  1:340637/1‑149 (MQ=255)
                                                                                  gTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCAt                                                              >  2:914920/1‑149 (MQ=255)
                                                                                  gTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCAt                                                              >  1:4439/1‑149 (MQ=255)
                                                                                   tttAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCAGCGCCACCATc                                                             >  1:814125/1‑149 (MQ=255)
                                                                                           aCGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCAttt                                                     <  1:795475/149‑1 (MQ=255)
                                                                                             gcgGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCAGCAAATCAGGATTAATCGCCGTCAATTCAGCGCAAGCAGAGTCATATTGCACAAGCTCCCCGCGTCCCGAGGACGCCAGCATGGACAAGATCAGCCAtttgt                                                   >  2:43665/1‑147 (MQ=255)
                                                                                               ggTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCt                                                 <  1:875858/149‑1 (MQ=255)
                                                                                               ggTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCt                                                 <  1:585185/149‑1 (MQ=255)
                                                                                                      aaTAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTAtgct                                          >  2:688374/1‑149 (MQ=255)
                                                                                                          aaaGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGctgctg                                      >  1:132665/1‑149 (MQ=255)
                                                                                                                aTCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTaa                                <  1:909590/149‑1 (MQ=255)
                                                                                                                 tCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCAGCATCAGGCNTTTTTCTTTATGCTGCTGTTGTaaa                               >  1:621073/1‑149 (MQ=255)
                                                                                                                 tCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTaaa                               >  2:191367/1‑149 (MQ=255)
                                                                                                                 tCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACAATCAGGCATTTTTCTTTATGCTACTGTTTTaaa                               >  2:132154/1‑149 (MQ=255)
                                                                                                                 tCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGCCCCGCGGACGCCAGCATCGCCACCATCCGGCATTTTTCTATATGCTGCTGTTGTaaa                               >  2:518134/1‑149 (MQ=255)
                                                                                                                     ggtggtGAATAATGCCGCTTTCGGACAATCCGGAATAATCGCCTGCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGc                           <  1:263109/149‑1 (MQ=255)
                                                                                                                      gtggtgAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGcc                          <  1:711655/149‑1 (MQ=255)
                                                                                                                       tggtgAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTGGTAAATCGCCa                         >  1:342012/1‑149 (MQ=255)
                                                                                                                       gggttAATAATGCCGCTTTCGGCCAATCCAGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCa                         <  2:615085/148‑1 (MQ=255)
                                                                                                                         gtgAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATa                       >  2:340786/1‑149 (MQ=255)
                                                                                                                         gtgAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATa                       >  1:837731/1‑149 (MQ=255)
                                                                                                                                 tGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGaca               >  1:884368/1‑149 (MQ=255)
                                                                                                                                           gggcAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCAgg     <  2:87698/146‑1 (MQ=255)
                                                                                                                                             ccAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCTACAACAAGTCAGAtt   >  2:724250/1‑149 (MQ=255)
                                                                                                                                              cAATCCGGATCTATCGCTGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCAGGTTg  <  1:362565/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                 
AGGGTTTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCAGGTTG  >  NC_000913_3_pae_tpiA/2679380‑2679670

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A