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
A4 F50 I2 R1 104 44.1 1376607 98.9% 1361464 150.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,892,270 A→G P19P (CCA→CCG)  queD → 6‑pyruvoyl tetrahydrobiopterin synthase (PTPS)

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,892,2700AG91.4% 112.6 / ‑4.4 35P19P (CCA→CCG) queD6‑pyruvoyl tetrahydrobiopterin synthase (PTPS)
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (17/15);  minor base C (3/0);  total (20/15)
Fisher's exact test for biased strand distribution p-value = 2.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

CAGCGATTTTGCGCAACAAAGTCGTTTTAGATAATGCGAAAAAACAGCCTTTCCGGTACTCTACGGCGGTTTTATCGTCCTGTAGAGAAATTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCACA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATCGATTTCGCTGAACTAAAAGCGGCGTTTAAACCAACCTACGA  >  NC_000913/2892122‑2892413
                                                                                                                                                    |                                                                                                                                                
cAGCGATTTTGCGCAACAAAGTCGTTTTAGATAATGCGAAAAAACAGCCTTTCCGGTACTCTACGGCGGTTTTATCGTCCTGTAGAGAAATTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACcgca                                                                                                                                                <  1:605741/151‑1 (MQ=255)
    gATTTTGCGCAACAAAGTCGTTTTAGATAATGCGAAAAAACAGCCTTTCCGGTACTCTACGGCGGTTTTATCGTCCTGTAGAGAAATTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTc                                                                                                                                           >  2:382843/1‑151 (MQ=255)
      ttttGCGCAACAAAGTCGTTTTAGATAATGCGAAAAAACAGCCTTTCCGGTACTCTACGGCGGTTTTTTTGTCATGTAGAGAAAATATGATGTCCACCCAGTTATTTTAAAATTTTACCTTCTAAGGCGCCCACCGCTTACCGCC‑CGTccc                                                                                                                                         >  1:343861/1‑151 (MQ=255)
       tttGCGCAACAAAGTCGTTTTAGATAATGCGAAAAAACAGCCTTTCCGGTACTCTACGGCGGTTTTATCGTCCTGTAGAGAAATTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTccc                                                                                                                                         <  2:306639/150‑1 (MQ=255)
                      cGTTTTAGATAATGCGAAAAAACAGCCTTTCCGGTACTCTACGGCGGTTTTATCTTCCTGTAGAGAAAATATGATGTTCACCACGTTTTTTTAAGATTTTACCTTCGAAGCCGCCCACCCCTTACCCCA‑CGTCCCGGGAGGGCATaaa                                                                                                                            >  2:151189/1‑148 (MQ=255)
                      cGTTTTAGATAATGCGAAAAAACAGCCTTTCCGGTACTCTACGGCGGTTTTATCGTCCTGTAGAGAAATTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAAtg                                                                                                                          <  2:400541/150‑1 (MQ=255)
                           tAGATAATGCGAAAAAACAGCCTTTCCGGTACTCTACGGCGGGTTTTTAGCCCTGTTAAGAAAATGGTATGGCCACCCAATTTTTTTAAAATTTTGCCTTTGAAGGCGCTGAACCCTTTCCCCACCGGCCCGGAgggggtaaaaatg                                                                                                                         >  1:664755/1‑138 (MQ=255)
                             gATAATGCGAAAAAACAGCCTTTCCGGTACTCTACGGCGGTTTTATCGTCCTGTAGAGAAATTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGcc                                                                                                                  <  2:559672/151‑1 (MQ=255)
                                  tGCGAAAAAACAGCCTTTCCGGTACTCTACGGCGGTTTTTTCGTCCTGTAGAGAAATTATGATGTCCACCACGTTATTTTAAGATTTCCCCTTCGAAGCCGCCCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCAc                                                                                                             >  2:548302/1‑151 (MQ=255)
                                          aaCAGCCTTTCCGGTACTCTACGGCGGTTTTATCGTCCTGTAGAGAAATTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTc                                                                                                     <  1:416422/151‑1 (MQ=255)
                                           aCAGCCTTTCCGGTACTCTACGGCGGTTTTTTCGTCCTGTTGAGAAATTTTTATGTCCCCCACGTTATTTTAAAATTTTAACCTCCAAGCCGCTCCCCCCTTACCCCA‑CCTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTcc                                                                                                    >  1:74999/1‑151 (MQ=255)
                                             aGCCTTTCCGGTACTCTACGGCGGTTTTATCGTCCTGTAGAGGAAATATGGTGTCCACCACGTTATTTTAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCCCGGGCATTCCtt                                                                                                  >  2:104243/1‑151 (MQ=255)
                                                                 gcggTTTTATCGTCCTGTAGAGAAATTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTa                                                                              <  1:826/151‑1 (MQ=255)
                                                                         aTCGTCCTGTAGAGAAATTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGaa                                                                      <  2:504245/151‑1 (MQ=255)
                                                                                tGTAGAGAAATTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATc                                                               >  1:70893/1‑151 (MQ=255)
                                                                                 gTAGAGAAATTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATcc                                                              >  2:506893/1‑151 (MQ=255)
                                                                                   agagAAATTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGc                                                            >  2:642016/1‑151 (MQ=255)
                                                                                        aaTTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACg                                                       <  1:379529/151‑1 (MQ=255)
                                                                                         aTTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACgg                                                      <  2:655425/151‑1 (MQ=255)
                                                                                            atgatgTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCt                                                   >  1:441008/1‑151 (MQ=255)
                                                                                                tgTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGAt                                               >  1:594885/1‑151 (MQ=255)
                                                                                                    caccacGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATc                                           <  2:106966/151‑1 (MQ=255)
                                                                                                       cacGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATCGAt                                        >  2:65471/1‑151 (MQ=255)
                                                                                                       cacGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATCGAt                                        >  2:9984/1‑151 (MQ=255)
                                                                                                              tttAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATCGATTTCGCTg                                 >  2:61929/1‑151 (MQ=255)
                                                                                                              tttAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATCGATTTCGCTg                                 >  1:286884/1‑151 (MQ=255)
                                                                                                                          aCCTTCGAAGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATCGATTTCGCTGAACTAAAAgcgg                     >  2:369511/1‑151 (MQ=255)
                                                                                                                                 aaGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATCGATTTCGCTGAACTAAAAGCGGCGTTTaa              <  1:423564/151‑1 (MQ=255)
                                                                                                                                  aGCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATCGATTTCGCTGAACTAAAAGCGGCGTTTaaa             <  1:311574/151‑1 (MQ=255)
                                                                                                                                   gCCGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATCGATTTCGCTGAACTAAAAGCGGCGTTTAaac            <  2:125200/151‑1 (MQ=255)
                                                                                                                                    ccGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATCGATTTCGCTGAACTAAAAGCGGCGTTTAaacc           <  1:678651/151‑1 (MQ=255)
                                                                                                                                     cGCTCACCGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATCGATTTCGCTGAACTAAAAGCGGCGTTTAaacca          <  2:432428/151‑1 (MQ=255)
                                                                                                                                            cGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTTGATCCGCATACGGGCTGGATTATCGATTTCGCTGAACTAAAAGCGGCGTTTAAACCAACCTACg   >  1:180135/1‑151 (MQ=255)
                                                                                                                                            cGCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGTTCCGCATACGGGCTGGATTATCGATTTCGCTGAACTAAAAGCGGCGTTTAAACCAACCTACg   >  1:550041/1‑151 (MQ=255)
                                                                                                                                             gCTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATCGATTTCGCTGAACTAAAAGCGGCGTTTAAACCAACCTACGa  <  1:451352/151‑1 (MQ=255)
                                                                                                                                              cTTACCGCA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATCGATTTCGCTGAACTAAAAGCGGCGTTTAAACCAACCTACg   >  1:340373/1‑149 (MQ=255)
                                                                                                                                                    |                                                                                                                                                
CAGCGATTTTGCGCAACAAAGTCGTTTTAGATAATGCGAAAAAACAGCCTTTCCGGTACTCTACGGCGGTTTTATCGTCCTGTAGAGAAATTATGATGTCCACCACGTTATTTAAAGATTTCACCTTCGAAGCCGCTCACCGCTTACCACA‑CGTCCCGGAAGGGCATAAATGTGGTCGCCTGCACGGGCATTCCTTTATGGTGCGACTGGAAATTACCGGGGAAGTCGATCCGCATACGGGCTGGATTATCGATTTCGCTGAACTAAAAGCGGCGTTTAAACCAACCTACGA  >  NC_000913/2892122‑2892413

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