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
A2 F50 I1 R1 170 39.5 1266514 99.2% 1256381 150.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,205,497 T→C pseudogene (1094/1134 nt) aaaE → pseudogene, phage terminase protein A family, e14 prophage;Phage or Prophage Related

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,205,4970TC100.0% 139.5 / NA 41pseudogene (1094/1134 nt)aaaEpseudogene, phage terminase protein A family, e14 prophage;Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/21);  total (20/21)

AACGTGGTCGGCAAAACCATTCCGGGTAACGATGATGTGGTGAAGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCTGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGCTGATTTATCCCCCGGCGGGTTTT  >  NC_000913/1205358‑1205641
                                                                                                                                           |                                                                                                                                                 
aaCGTGGTCGGCAAAACCATTCCGGGTAACGATGATGTGGTGAAGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATcaca                                                                                                                                        <  2:279932/151‑1 (MQ=255)
        cGGCAAAACCATTCCGGGTAACGATGATGTGGTGAAGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑Tc                                                                                                                                <  1:29699/150‑1 (MQ=255)
          gCAAAACCATTCCGGGTAACGATGATGTGGTGAAGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTa                                                                                                                             <  1:23879/151‑1 (MQ=255)
           cAAAACCATTCCGGGTAACGATGATGTGGTGAAGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGGTTGGAGAGGCCTGCTGTTCGAGGAAAAAGAAACGCCGCCTGGTTACAtt                                                                                                                                      >  2:493688/1‑142 (MQ=255)
               aCCATTCCGGGTAACGATGATGTGGTGAAGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGa                                                                                                                        <  1:381479/151‑1 (MQ=255)
                 cATTCCGGGTAACGATGATGTGGTGAAGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGGAGAGGCACGCTGTACGAGAAAAAAAAAAACCCCGCTGGTCACATTTAG‑TCCTTCGGGATc                                                                                                                      >  1:12874/1‑151 (MQ=255)
                     ccGGGTAACGATGATGTGGTGAAGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCcgc                                                                                                                   <  2:63198/150‑1 (MQ=255)
                             cGATGATGTGGTGAAGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTaa                                                                                                          <  1:54227/151‑1 (MQ=255)
                                 gatgTGGTGAAGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGGAGAGCCCTGCTGTACGAGAAAAAAGAAACGCCGTCTGATCACATTTAG‑TCCTACGGGGTCCGCTCGCttt                                                                                                            >  1:43692/1‑145 (MQ=255)
                                 gatgTGGTGAAGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTg                                                                                                       <  2:7373/150‑1 (MQ=255)
                                  atgTGGTGAAGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAg                                                                                                     <  2:62214/151‑1 (MQ=255)
                                      ggtgAAGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTa                                                                                                  <  2:297943/150‑1 (MQ=255)
                                           aGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATg                                                                                            <  1:483518/151‑1 (MQ=255)
                                             cccGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTTGGAGAGAGCTGCGGTACGAGAAAGAAAAAACCCCGCCTGGTCACATTTAGTTCCTA‑GGGGGCCGCCCGCTTTTACTGAGGGGATTAt                                                                                             >  1:118397/1‑148 (MQ=255)
                                              ccGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATc                                                                                         <  1:223980/151‑1 (MQ=255)
                                                   aaGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGGAGAGGCCCGCTGTACGAGAAAAAAAACACCCCGGCTGGTCACATTTAG‑TCCTACGGGGGCCCCCCGCCTTTAATGAGGGAAATATTATTATGCt                                                                                    >  1:381096/1‑151 (MQ=255)
                                                    aGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTg                                                                                   <  1:493698/151‑1 (MQ=255)
                                                      gAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGAt                                                                                 <  1:401611/151‑1 (MQ=255)
                                                          aGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGGAGAGCCATGCTGTACGAGAAAAAAAAAACGCCGTCTGATCACATTGAG‑TCCTACCGGGTACCCCCGCTTTTACTGAGGGAATTATTATCATTCttgtttt                                                                              >  1:46383/1‑144 (MQ=255)
                                                              ggAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGATTGCAGAGGCCCGCTGTACGAGGAAAAAAAAACACCGACTGAACACAATTAT‑TCCTACGGGATCCGCCCGCTTTTAATGAGGGAAATATGATCAAGCTGGtttt                                                                              >  1:289590/1‑144 (MQ=255)
                                                                                 gCAGTTGCGCTGATTATGGCGGTTGGGAGAGGCATGCCGTTCGGGAAAGAAGAAAAGCCGCCTGATCAAAATTAG‑TCCTACGGGGTCCGCCCGCTTTTACTGAGGGAAATATTATCATGCTGATTTTCGCGCCCCTGGTGGGGGGGGTggg                                                      >  1:238955/1‑151 (MQ=255)
                                                                                  cAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGt                                                     <  2:209692/151‑1 (MQ=255)
                                                                                    gTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTgc                                                   <  1:410999/151‑1 (MQ=255)
                                                                                                  ggCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGt                                     <  2:448144/151‑1 (MQ=255)
                                                                                                     ggTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATg                                  <  2:365577/151‑1 (MQ=255)
                                                                                                     ggTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATg                                  >  1:32465/1‑151 (MQ=255)
                                                                                                              agCCATGCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGc                         >  1:576300/1‑151 (MQ=255)
                                                                                                                    gCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTgc                                                   <  2:401471/119‑1 (MQ=255)
                                                                                                                    gCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTgc                                                   >  1:401478/1‑119 (MQ=255)
                                                                                                                    gCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGCTGAttt                   >  2:554306/1‑151 (MQ=255)
                                                                                                                    gCTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGCTGAtt                    <  2:169597/150‑1 (MQ=255)
                                                                                                                     cTGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGCTGAttt                   >  1:97081/1‑150 (MQ=255)
                                                                                                                      tGTACGAGAAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGCTGATTTAt                 >  2:285736/1‑151 (MQ=255)
                                                                                                                           gagaAAGAAGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGCTGATTTATccccc            <  2:146923/151‑1 (MQ=255)
                                                                                                                            agaaagaaGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGCTGATTTATCCCCcg           >  2:487176/1‑151 (MQ=255)
                                                                                                                            agaaagaaGACACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGCTGATTTATCCCCcg           >  1:494479/1‑151 (MQ=255)
                                                                                                                                agaagaCACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGCTGATTTATCCCCcggcgg       >  1:7495/1‑151 (MQ=255)
                                                                                                                                agaagaCACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGCTGATTTATCCCCcggcg        <  1:72913/150‑1 (MQ=255)
                                                                                                                                agaagaCACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGCTGATTTATCCCCcggcg        >  2:72913/1‑150 (MQ=255)
                                                                                                                                 gaagaCACGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGCTGATTTATCCCCCGGCggg      >  1:157759/1‑151 (MQ=255)
                                                                                                                                      cacGCCGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGCTGATTTATCCCCCGGCGGGtttt  >  1:285295/1‑150 (MQ=255)
                                                                                                                                           |                                                                                                                                                 
AACGTGGTCGGCAAAACCATTCCGGGTAACGATGATGTGGTGAAGCCCGTCAAGGAGCAGGCGGAAAACAAAATCGATGGTGCAGTTGCGCTGATTATGGCGGTTGGCAGAGCCATGCTGTACGAGAAAGAAGACACGCTGTCTGATCACATTGAG‑TCCTACGGGATCCGCTCGCTTTAACTGAGGTAATTATGATCATGCTGATTCTCGCGCCTCTGGTGGGCGTGCTGGGTGCGCTTTTGCTGGCGTATGGTGCCTGGCTGATTTATCCCCCGGCGGGTTTT  >  NC_000913/1205358‑1205641

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A