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
A34 F5 I0 R1 408 67.6 2494072 96.8% 2414261 139.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,180,043 C→T 100% T408M (ACG→ATG)  yegT → nucleoside transporter, low affinity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,180,0430CT96.6% 204.2 / ‑2.1 59T408M (ACG→ATG) yegTnucleoside transporter, low affinity
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base T (24/33);  total (25/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GATGATGGAAAAGATGTTCGCTTATCAGGAACCGGTAAACGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTACGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAGGGGATGCGATGGGGATGCCCTCCGAGCTTTGGCCACGCAGCCGCGTTAAA  >  NC_000913/2179897‑2180190
                                                                                                                                                  |                                                                                                                                                   
gatgatGGAAAAGATGTTCGCTTATCAGGAACCGGTAAACGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATgg                                                                                                                                                   <  4:258944/149‑1 (MQ=255)
 atgatgGAAAAGATGTTCGCTTATCAGGAACCGGTAAACGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGc                                                                                                                                                  <  4:585933/149‑1 (MQ=255)
   gatgGAAAAGATGTTCGCTTATCAGGAACCGGTAAACGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTa                                                                                                                                                <  2:465015/149‑1 (MQ=255)
     tgGAAAAGATGTTCGCTTATCAGGAACCGGTAAACGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATc                                                                                                                                              >  3:150075/1‑149 (MQ=255)
      ggAAAAGATGTTCGCTTATCAGGAACCGGTAAACGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTACGGCTATCa                                                                                                                                             >  4:600674/1‑149 (MQ=255)
            gATGTTCGCTTATCAGGAACCGGTAAACGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCg                                                                                                                                       >  2:24818/1‑149 (MQ=255)
                   gCTTATCAGGAACCGGTAAACGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATcg                                                                                                                                <  2:598668/149‑1 (MQ=255)
                   gCTTATCAGGAACCGGTAAACGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATcg                                                                                                                                >  2:363702/1‑149 (MQ=255)
                      tATCAGGAACCGGTAAACGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGa                                                                                                                             <  2:193121/149‑1 (MQ=255)
                        tCAGGAACCGGTAAACGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGata                                                                                                                           >  2:157377/1‑149 (MQ=255)
                                 ggTAAACGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGa                                                                                                                  >  1:187144/1‑149 (MQ=255)
                                       cGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAg                                                                                                            <  4:82875/149‑1 (MQ=255)
                                       cGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAg                                                                                                            <  2:352979/149‑1 (MQ=255)
                                          actgactTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAgggg                                                                                                         >  3:550431/1‑149 (MQ=255)
                                          actgactTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAgggg                                                                                                         >  2:585694/1‑149 (MQ=255)
                                          actgactTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAgggg                                                                                                         <  3:87763/149‑1 (MQ=255)
                                            tgactTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGaa                                                                                                       <  2:515674/149‑1 (MQ=255)
                                            tgactTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGaa                                                                                                       <  3:457740/149‑1 (MQ=255)
                                            tgactTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGaa                                                                                                       >  2:83305/1‑149 (MQ=255)
                                                tttCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTa                                                                                                   >  4:126892/1‑149 (MQ=255)
                                                tttCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTa                                                                                                   >  1:610342/1‑149 (MQ=255)
                                                  tCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTaaa                                                                                                 <  3:574282/149‑1 (MQ=255)
                                                     aCTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGa                                                                                              >  3:187689/1‑149 (MQ=255)
                                                      cTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGTTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGTCTATCAAGGTCGATGAACGCGATATTGCGTTGACACAAGGGGCAGTTAAATGaa                                                                                             <  2:236441/149‑1 (MQ=255)
                                                      cTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGaa                                                                                             <  2:401660/149‑1 (MQ=255)
                                                        ggTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGaaaa                                                                                           <  2:610342/149‑1 (MQ=255)
                                                                  gtgGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAAt                                                                                                <  4:465620/134‑1 (MQ=255)
                                                                  gtgGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAAt                                                                                                >  3:465620/1‑134 (MQ=255)
                                                                     gACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCgat                                                                                                                                     <  2:343532/94‑1 (MQ=255)
                                                                     gACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCgat                                                                                                                                     >  1:343532/1‑94 (MQ=255)
                                                                       cTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCg                                                                            <  1:102820/149‑1 (MQ=255)
                                                                               gcgGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCtt                                                                    >  2:227410/1‑149 (MQ=255)
                                                                                  gTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTAt                                                                 <  1:343308/149‑1 (MQ=255)
                                                                                   tgatgaTTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATg                                                                <  1:227410/149‑1 (MQ=255)
                                                                                   tgatgaTTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATg                                                                <  2:23476/149‑1 (MQ=255)
                                                                                    gatgatTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCTATAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGTAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTAggg                                                               <  2:257856/149‑1 (MQ=255)
                                                                                         ttGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAGGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAgg                                                          >  4:61153/1‑149 (MQ=255)
                                                                                             cATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGtt                                                      >  4:472018/1‑149 (MQ=255)
                                                                                               ttATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAg                                                    <  1:24818/149‑1 (MQ=255)
                                                                                                 aTCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAggg                                                  <  1:83305/149‑1 (MQ=255)
                                                                                                        tGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATTGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTGTATGGGCAGGCGTTAGGGGATGCGa                                           <  4:521214/149‑1 (MQ=255)
                                                                                                          cTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAGGGGATGCGATg                                         <  2:214858/149‑1 (MQ=255)
                                                                                                             ttCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTAt                                                                                 >  4:369722/1‑106 (MQ=255)
                                                                                                             ttCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTAt                                                                                 <  1:9204/106‑1 (MQ=255)
                                                                                                             ttCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTAt                                                                                 >  2:9204/1‑106 (MQ=255)
                                                                                                             ttCATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTAt                                                                                 <  3:369722/106‑1 (MQ=255)
                                                                                                               cATGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAGGGGATGCGATGGGGAt                                    <  3:541774/149‑1 (MQ=255)
                                                                                                                aTGATTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAGGGGATGCGATGGGGATg                                   >  2:434624/1‑149 (MQ=255)
                                                                                                                   aTTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGaa                                                                                             <  2:8133/88‑1 (MQ=255)
                                                                                                                   aTTTTTTTCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGaa                                                                                             >  1:8133/1‑88 (MQ=255)
                                                                                                                        tttCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAGGGGATGCGATGGGGATGCCCTCCGa                           <  4:187689/149‑1 (MQ=255)
                                                                                                                        tttCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAGGGGATGCGATGGGGATGCCCTCCGa                           <  2:381300/149‑1 (MQ=255)
                                                                                                                         ttCCGCGAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAGGGGATGCGATGGGGATGCCCTCCGAg                          <  1:363702/149‑1 (MQ=255)
                                                                                                                            cgcgAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAGGGGATGCGATGGGGATGCCCTCCGAGCtt                       <  2:236711/149‑1 (MQ=255)
                                                                                                                             gcgAATCCGACAACGAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAGGGGATGCGATGGGGATGCCCTCCGAGCttt                      >  1:274025/1‑149 (MQ=255)
                                                                                                                                           gAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAGGGGATGCGATGGGGATGCCCTCCGAGCTTTGGCCACGCAGCcgc        >  2:489678/1‑149 (MQ=255)
                                                                                                                                           gAAATTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAGGGGATGCGATGGGGATGCCCTCCGAGCTTTGGCCACGCAGCcgc        >  4:544199/1‑149 (MQ=255)
                                                                                                                                              aTTATGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAGGGGATGCGATGGGGATGCCCTCCGAGCTTTGGCCACGCAGCCGCGtt     >  2:57187/1‑149 (MQ=255)
                                                                                                                                                 aCGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGAAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTATTTATGGGCAGGCGTTAGGGGATGCGATGGGGATGCCCTCCGAGCTTTGGCCACGCAGCCGCGTTaaa  <  3:600674/149‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                                                   
GATGATGGAAAAGATGTTCGCTTATCAGGAACCGGTAAACGGACTGACTTTCAACTGGTCCGGGATGTGGACTTTCGGCGCGGTGATGATTGCCATTATCGCCGTGCTGTTCATGATTTTTTTCCGCGAATCCGACAACGAAATTACGGCTATCAAGGTCGATGATCGCGATATTGCGTTGACACAAGGGGAAGTTAAATGAAAACAGAACGTATTCTCGGTGCTCTTTATGGGCAGGCGTTAGGGGATGCGATGGGGATGCCCTCCGAGCTTTGGCCACGCAGCCGCGTTAAA  >  NC_000913/2179897‑2180190

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A