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
A3 F1 I2 R1 58 36.1 1832140 90.7% 1661750 105.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,763,869 (T)7→8 coding (1285/1617 nt) yfjL ← CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,763,8621.T97.9% 155.8 / ‑3.6 47coding (1292/1617 nt)yfjLCP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base T (24/22);  total (25/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

TAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑TTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCACCTTCTGG  >  NC_000913/2763737‑2763995
                                                                                                                              |                                                                                                                                      
tAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTgcgcg                                                                                                                           >  1:508769/1‑139 (MQ=255)
 agagTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTgcgcgc                                                                                                                          <  1:258614/139‑1 (MQ=255)
     tCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTa                                                                                                                      >  2:260168/1‑139 (MQ=255)
        tAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGGCTTTCATGTCGAGGATTTT‑TTTTGCGCGCGGTATCg                                                                                                                   >  2:545547/1‑139 (MQ=255)
          gCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGAt                                                                                                                 >  2:219095/1‑139 (MQ=255)
                      aacaAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑ttt‑tttttg                                                                                                                              >  2:82502/1‑111 (MQ=255)
                      aacaAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑ttt‑tttttg                                                                                                                              <  1:82502/113‑3 (MQ=255)
                          aaCGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc                                                                                                 <  1:219095/139‑1 (MQ=255)
                                aaaCGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTgcgcg                                                                                                                           >  2:717082/1‑107 (MQ=255)
                                aaaCGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTgcgcg                                                                                                                           <  1:717082/107‑1 (MQ=255)
                                    gATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACt                                                                                       <  2:508769/139‑1 (MQ=255)
                                     aTCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc                                                                                                 <  2:757338/128‑1 (MQ=255)
                                     aTCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc                                                                                                 >  1:757338/1‑128 (MQ=255)
                                         aGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTgcgcg                                                                                                                           <  2:60258/98‑1 (MQ=255)
                                         aGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTgcgcg                                                                                                                           >  1:60258/1‑98 (MQ=255)
                                              aGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTgcgcg                                                                                                                           >  1:775195/1‑93 (MQ=255)
                                              aGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTAt                                                                             >  2:318389/1‑139 (MQ=255)
                                              aGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCAAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTgcgcg                                                                                                                           <  2:775195/93‑1 (MQ=255)
                                              aGCATCGAAAGGTTGGCTACCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc                                                                                                 >  2:495640/1‑119 (MQ=255)
                                              aGCATCGAAAGGTTGGCTACCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc                                                                                                 <  1:495640/119‑1 (MQ=255)
                                                    gAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTAt                                                                             >  2:242885/1‑133 (MQ=255)
                                                    gAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTAt                                                                             <  1:242885/133‑1 (MQ=255)
                                                     aaaGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTAt                                                                                                                     <  2:654807/92‑1 (MQ=255)
                                                     aaaGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑TTTATTTTGCGCGCGGTAt                                                                                                                     >  1:654807/1‑92 (MQ=255)
                                                            ggCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGa                                                               >  1:574948/1‑139 (MQ=255)
                                                             gCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGAc                                                              >  2:507347/1‑139 (MQ=255)
                                                                gCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGc                                                           <  1:318389/139‑1 (MQ=255)
                                                                gCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑ttt‑tttttgcg                                                                                                                            <  1:264488/73‑5 (MQ=255)
                                                                gCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑ttt‑tttttgcg                                                                                                                            >  2:264488/1‑69 (MQ=255)
                                                                 ccATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa                                                          <  2:607228/139‑1 (MQ=255)
                                                                 ccATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa                                                          <  2:725703/139‑1 (MQ=255)
                                                                        gAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCTATCTGACGGCAATGTTaa                                                   <  1:507347/139‑1 (MQ=255)
                                                                              cGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCg                                                                                              >  1:379517/1‑90 (MQ=255)
                                                                              cGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCg                                                                                              <  2:379517/90‑1 (MQ=255)
                                                                                tCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATccc                                                                                 >  2:274854/1‑101 (MQ=255)
                                                                                tCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATccc                                                                                 <  1:274854/101‑1 (MQ=255)
                                                                                         tGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCg                                  >  1:30028/1‑139 (MQ=255)
                                                                                                          aTCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGtt                                                     <  2:445523/103‑1 (MQ=255)
                                                                                                          aTCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGtt                                                     >  1:445523/1‑103 (MQ=255)
                                                                                                           tCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGt                                            >  2:429119/1‑111 (MQ=255)
                                                                                                           tCGTCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGt                                            <  1:429119/111‑1 (MQ=255)
                                                                                                              tCTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGa             >  2:484135/1‑139 (MQ=255)
                                                                                                               cTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGt                                                                                                   >  2:174329/1‑52 (MQ=39)
                                                                                                               cTTTAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGt                                                                                                   <  1:174329/52‑1 (MQ=39)
                                                                                                                tttAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGaa                                                                                                       >  2:331836/1‑47 (MQ=38)
                                                                                                                tttAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGaa                                                                                                       <  1:331836/47‑1 (MQ=38)
                                                                                                                tttAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAAc                                     >  1:735956/1‑113 (MQ=255)
                                                                                                                tttAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAAc                                     <  2:735956/113‑1 (MQ=255)
                                                                                                                tttAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATc           <  1:484135/139‑1 (MQ=255)
                                                                                                                  tAATGTCGAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACAAACTCGCTGAAGCAAATCCAAAGCTGATCAc         >  2:90722/1‑139 (MQ=255)
                                                                                                                         gAGGATTTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCACCTTCTgg  >  2:715769/1‑139 (MQ=255)
                                                                                                                              |                                                                                                                                      
TAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑TTT‑TTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCACCTTCTGG  >  NC_000913/2763737‑2763995

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A