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
A13 F1 I2 R1 92 50.6 2362856 94.3% 2228173 111.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,594,256 (C)8→9 pseudogene (3732/3861 nt) yneO ← pseudogene, AidA homolog

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,594,2481.C100.0% 142.1 / NA 39pseudogene (3740/3861 nt)yneOpseudogene, AidA homolog
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (24/15);  total (24/15)

CCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAG  >  NC_000913/1594152‑1594377
                                                                                                 |                                                                                                                                  
ccTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGaa                                                                                          >  1:827669/1‑139 (MQ=255)
  tGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATc                                                                                        <  1:155243/139‑1 (MQ=255)
    cAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCgt                                                                                      >  2:1061122/1‑139 (MQ=255)
         gtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTa                                                                                 >  1:292801/1‑139 (MQ=255)
         gtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTa                                                                                 >  2:674118/1‑139 (MQ=255)
              aTTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGt                                                                            >  1:902831/1‑139 (MQ=255)
                 tCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAg                                                                         <  2:827669/139‑1 (MQ=255)
                      aCATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATcc                                                                    <  1:468707/139‑1 (MQ=255)
                            cacCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTAc                                                              >  1:672099/1‑139 (MQ=255)
                            cacCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑‑cccccc                                                                                                                             <  1:493963/75‑1 (MQ=255)
                            cacCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑‑cccccc                                                                                                                             >  2:493963/1‑75 (MQ=255)
                                 cTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCCCGATATCGGTCTTACCTTGATACGCCGCGGAATCGTTTTTACGAGCCAGGATCCCGGTACCCAGt                                                         >  1:472061/1‑139 (MQ=255)
                                 cTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGt                                                         >  2:69662/1‑139 (MQ=255)
                                 cTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGt                                                         <  1:1061122/139‑1 (MQ=255)
                                  tGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑‑ccccccccc                                                                                                                          >  2:239180/1‑71 (MQ=255)
                                  tGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑‑ccccccccc                                                                                                                          <  1:239180/72‑2 (MQ=255)
                                      tttgATATTAATGTGTTGACTTGCCATATTAATGGGAGAGTCGGAACCGAAAACCATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGt                                                    <  1:665718/136‑1 (MQ=255)
                                           tatTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACAt                                               <  2:292801/139‑1 (MQ=255)
                                              tAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCac                                            >  2:679265/1‑139 (MQ=255)
                                                  gtgtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgct                                        <  1:69662/139‑1 (MQ=255)
                                                   tgtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgcta                                       >  2:908525/1‑139 (MQ=255)
                                                    gtTGACTTGGCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctac                                      <  1:679265/139‑1 (MQ=255)
                                                     ttGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctacc                                     >  1:505901/1‑139 (MQ=255)
                                                     ttGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGGTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctacc                                     >  1:24376/1‑139 (MQ=255)
                                                      tGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctaccg                                    >  1:854417/1‑139 (MQ=255)
                                                             ccATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGa                                                                                                      >  1:282954/1‑66 (MQ=255)
                                                             ccATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGa                                                                                                      <  2:282954/66‑1 (MQ=255)
                                                                      tGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCa                    >  1:780570/1‑139 (MQ=255)
                                                                       ggCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTa                                                                                 <  2:1130409/77‑1 (MQ=255)
                                                                       ggCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTa                                                                                 >  1:1130409/1‑77 (MQ=255)
                                                                       ggCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCAt                   >  1:581240/1‑139 (MQ=255)
                                                                       ggCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTAAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCAt                   >  1:688334/1‑139 (MQ=255)
                                                                          agagTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGa                                                                       >  2:187818/1‑84 (MQ=255)
                                                                          agagTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGa                                                                       <  1:187818/84‑1 (MQ=255)
                                                                           gagTCGGAACCGAAAGCAATTTCCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGc                >  2:444192/1‑139 (MQ=255)
                                                                           gagTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGa                                >  2:515940/1‑122 (MQ=255)
                                                                           gagTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGa                                <  1:515940/122‑1 (MQ=255)
                                                                           gagTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGcc               <  2:581240/139‑1 (MQ=255)
                                                                            agTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGccc              >  1:135942/1‑139 (MQ=255)
                                                                                ggAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCt          <  2:688334/139‑1 (MQ=255)
                                                                                       aaaGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgct                                        <  2:1086840/102‑1 (MQ=255)
                                                                                       aaaGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgct                                        >  1:1086840/1‑102 (MQ=255)
                                                                                        aaGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAg  >  2:230768/1‑139 (MQ=255)
                                                                                                 |                                                                                                                                  
CCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAG  >  NC_000913/1594152‑1594377

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A