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 F195 I0 R2 483 52.1 1908604 98.1% 1872340 138.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,324,837 A→C 14.6% Y31S (TAT→TCT) ‡ yciQ → enhancer of membrane protein expression; putative inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,324,8370AC14.6% 110.2 / 11.8 41Y31S (TAT→TCT) ‡yciQenhancer of membrane protein expression; putative inner membrane protein
Reads supporting (aligned to +/- strand):  ref base A (21/14);  new base C (3/3);  total (24/17)
Fisher's exact test for biased strand distribution p-value = 6.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAGGTGATGTGAAGCCTTTCTTATAACAAATTGCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATCGTGATTTACCACGACTATGGATGCAGC  >  NC_000913/1324692‑1324983
                                                                                                                                                  |                                                                                                                                                  
gTAGGTGATGTGAAGCCTTTCTTATAACAAATTGCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATga                                                                                                                                                 <  4:192613/149‑1 (MQ=255)
 tAGGTGATGTGAAGCCTTTCTTATAACAAATTGCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATgaa                                                                                                                                                >  2:189383/1‑149 (MQ=255)
    gTGATGTGAAGCCTTTCTTATAACAAATTGCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATgaagaa                                                                                                                                             <  1:15045/149‑1 (MQ=255)
          tgAAGCCTTTCTTATAACAAATTGCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGAtc                                                                                                                                       <  1:231614/149‑1 (MQ=255)
           gAAGCCTTTCTTATAACAAATTGCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCATGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑CATAAGAAggg                                                                                                                                          >  1:23293/1‑145 (MQ=255)
           gAAGCCTTTCTTATAACAAATTGCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑CATAAGAAggg                                                                                                                                          <  2:23293/145‑1 (MQ=255)
            aaGCCTTTCTTATAACAAATTGCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCACTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGAtctc                                                                                                                                     <  2:196461/149‑1 (MQ=255)
                     ttATAACAAATTGCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑CATAAGAAGGGAtctccgtgt                                                                                                                                <  1:455318/145‑6 (MQ=255)
                     ttATAACAAATTGCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑CATAAGAAGGGAtctccgtgt                                                                                                                                >  2:455318/1‑140 (MQ=255)
                        taACAAATTGCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGt                                                                                                                         >  3:415453/1‑149 (MQ=255)
                             aaTTGCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAg                                                                                                                    >  4:59084/1‑149 (MQ=255)
                               ttGCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGTGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGcc                                                                                                                  >  3:400816/1‑149 (MQ=255)
                                 gCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCCGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCAc                                                                                                                <  4:400816/149‑1 (MQ=255)
                                       cACGGATGGAAGATTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTACCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑CATaagaag                                                                                                                                            <  1:232268/115‑1 (MQ=255)
                                       cACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTACCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑CATaagaag                                                                                                                                            >  2:232268/1‑115 (MQ=255)
                                        aCGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCaa                                                                                                         >  4:62502/1‑149 (MQ=255)
                                                 aGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATggg                                                                                                >  1:8831/1‑149 (MQ=255)
                                                         gCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGa                                                                                        >  2:408797/1‑149 (MQ=255)
                                                           aGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACa                                                                                      <  2:396276/149‑1 (MQ=255)
                                                                                  tGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAg                                                               >  1:69453/1‑149 (MQ=255)
                                                                                    ttGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGgc                                                             >  3:6161/1‑149 (MQ=255)
                                                                                      gATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGgcgc                                                           >  2:157230/1‑149 (MQ=255)
                                                                                         aGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGaa                                                        >  2:126057/1‑149 (MQ=255)
                                                                                                   tttGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGAt                                              <  1:408797/149‑1 (MQ=255)
                                                                                                         tcatcTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCa                                        <  4:205778/149‑1 (MQ=255)
                                                                                                              tctAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCt                                   >  1:129728/1‑149 (MQ=255)
                                                                                                               ctAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCtt                                  <  4:415453/149‑1 (MQ=255)
                                                                                                                    ttATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATc                             <  2:129728/149‑1 (MQ=255)
                                                                                                                          aGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATCGTGAtt                       >  2:151161/1‑149 (MQ=255)
                                                                                                                           gAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATCGTGAttt                      >  1:92602/1‑149 (MQ=255)
                                                                                                                                      gaTCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATCGTGATTTACCACGACTAt           <  2:8831/149‑1 (MQ=255)
                                                                                                                                       aTCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATCGTGATTTACCACGACTATg          >  3:255475/1‑149 (MQ=255)
                                                                                                                                       aTCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATCGTGATTTACCACGACTATg          <  1:189383/149‑1 (MQ=255)
                                                                                                                                        tCCCTTCTTCAT‑AAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATCGTGATTTACCACGACTATgg         >  1:150344/1‑149 (MQ=255)
                                                                                                                                         cccTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATCGTGa                         <  3:329041/132‑1 (MQ=255)
                                                                                                                                         cccTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATCGTGa                         >  4:329041/1‑132 (MQ=255)
                                                                                                                                         cccTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATCGTGATTTACCACGACTATGGa        <  2:69453/149‑1 (MQ=255)
                                                                                                                                         cccTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATCGTGATTTACCACGACTATGGa        >  1:148344/1‑149 (MQ=255)
                                                                                                                                          ccTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAATCACGGCTTTTATCGTGATTTACCACGACTATGGAt       >  4:310550/1‑149 (MQ=255)
                                                                                                                                              ctt‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATCGTGATTTACCACGACTATGGATGCAg   >  3:50627/1‑149 (MQ=255)
                                                                                                                                               tt‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATCGTGATTTACCACGACTATGGATGCAGc  >  1:73863/1‑149 (MQ=255)
                                                                                                                                                  |                                                                                                                                                  
GTAGGTGATGTGAAGCCTTTCTTATAACAAATTGCGTTCCACGGATGGAAGACTATGGCAGGGAAGTTTCGCTGCATTTTGCTGTTGATAGCAGGGCTGTTTGTATCATCTCTAAGTTATGCAGAAAACACGGAGATCCCTTCTT‑ATGAAGAAGGGATCTCGCTCTTTGATGTTGAAGCCACTCTGCAACCAGATGGGGTGCTCGACATCAAAGAAAATATTCATTTTCAGGCGCGAAATCAGCAGATTAAGCACGGCTTTTATCGTGATTTACCACGACTATGGATGCAGC  >  NC_000913/1324692‑1324983

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A