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
A13 F69 I0 R1 1426 148.0 5875178 97.4% 5722423 123.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 294,915 T→A 6.8% intergenic (‑116/+224) yagM ← / ← yagN CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913294,9150TA 6.8% 208.6 / 4.3 59intergenic (‑116/+224)yagM/yagNCP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base T (31/24);  new base A (2/2);  total (33/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

AAAATTAGTAACACTATTAGACATTTTTAAGGAAACCTCTTTGTTATCTCAATATAAAACTACTATCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGAATGGTTTGAGAT  >  NC_000913/294776‑295062
                                                                                                                                           |                                                                                                                                                   
aaaaTTAGTAACACTATTAGACATTTTTAAGGAAACCTCTTTGTTATCTCAATATAAAACTACTATCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGa                                                                                                                                            >  1:1367820/1‑149 (MQ=255)
      aGTAACACTATTAGACATTTTTAAGGAAACCTCTTTGTTATCTCAATATAAAACTACTATCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTtct                                                                                                                                      <  2:1367820/149‑1 (MQ=255)
            acTATTAGACATTTTTAAGGAAACCTCTTTGTTATCTCAATATAAAACTACTATCTTAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACa                                                                                                                                >  2:606111/1‑149 (MQ=255)
                 tAGACATTTTTAAGGAAACCTCTTTGTTATCTCAATATAAAACTACTATCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGaaaa                                                                                                                           <  4:115223/149‑1 (MQ=255)
                       tttttAAGGAAACCTCTTTGTTATCTCAATATAAAACTACTATCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAAt                                                                                                                          <  3:1329726/144‑1 (MQ=255)
                       tttttAAGGAAACCTCTTTGTTATCTCAATATAAAACTACTATCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAAt                                                                                                                          >  4:1329726/1‑144 (MQ=255)
                                 aaCCTCTTTGTTATCTCAATATAAAACTACTATCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTAt                                                                                                                      <  1:1298540/138‑1 (MQ=255)
                                 aaCCTCTTTGTTATCTCAATATAAAACTACTATCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTAt                                                                                                                      >  2:1298540/1‑138 (MQ=255)
                                    ctctTTGTTATCTCAATATAAAACTACTATCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTAt                                                                                                                      >  1:184820/1‑135 (MQ=255)
                                    ctctTTGTTATCTCAATATAAAACTACTATCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTAt                                                                                                                      <  2:184820/135‑1 (MQ=255)
                                     tctTTGTTATCTCAATATAAAACTACTATCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGa                                                                                                       >  1:269446/1‑149 (MQ=255)
                                            tATCTCAATATAAAACTACTATCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCttt                                                                                                <  2:269446/149‑1 (MQ=255)
                                                            tactaTCTTAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATgg                                                                                <  1:606111/149‑1 (MQ=255)
                                                            tactaTCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGt                                                                                                                        >  4:1432506/1‑109 (MQ=255)
                                                            tactaTCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGt                                                                                                                        <  3:1432506/109‑1 (MQ=255)
                                                                              aGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCg                                                                                                                                    <  1:491423/79‑1 (MQ=255)
                                                                              aGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCg                                                                                                                                    >  2:491423/1‑79 (MQ=255)
                                                                                      cccATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTgg                                                            <  2:381773/143‑1 (MQ=255)
                                                                                      cccATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTgg                                                            >  1:381773/1‑143 (MQ=255)
                                                                                      cccATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAgg                                                      >  3:619831/1‑149 (MQ=255)
                                                                                       ccATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATttat                                                                                                                                                  <  3:384588/56‑1 (MQ=255)
                                                                                       ccATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATttat                                                                                                                                                  >  4:384588/1‑56 (MQ=255)
                                                                                       ccATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGtttt                                                              <  4:139571/140‑1 (MQ=255)
                                                                                       ccATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGtttt                                                              >  3:139571/1‑140 (MQ=255)
                                                                                        cATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTTTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTa                                                    >  2:599963/1‑149 (MQ=255)
                                                                                         aTTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACa                                                                                                                                <  2:384043/72‑1 (MQ=255)
                                                                                         aTTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACa                                                                                                                                >  1:384043/1‑72 (MQ=255)
                                                                                          tttttCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAg                                                   >  3:220527/1‑148 (MQ=255)
                                                                                          tttttCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAg                                                   <  4:220527/148‑1 (MQ=255)
                                                                                                   gggCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAAt                                                                                  <  2:151381/108‑1 (MQ=255)
                                                                                                   gggCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAAt                                                                                  >  1:151381/1‑108 (MQ=255)
                                                                                                          aTCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGt                                  >  4:1247097/1‑149 (MQ=255)
                                                                                                           tCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTa                                                                                    >  2:634905/1‑98 (MQ=255)
                                                                                                           tCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTa                                                                                    <  1:634905/98‑1 (MQ=255)
                                                                                                           tCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTc                                 <  3:1247097/149‑1 (MQ=255)
                                                                                                               tataAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGa                                                                      <  1:489356/108‑1 (MQ=255)
                                                                                                               tataAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGa                                                                      >  2:489356/1‑108 (MQ=255)
                                                                                                                     tCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGc                       >  2:517032/1‑149 (MQ=255)
                                                                                                                         tAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGc                                                  >  3:1092158/1‑118 (MQ=255)
                                                                                                                         tAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGc                                                  <  4:1092158/118‑1 (MQ=255)
                                                                                                                         tAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCAtt                   >  4:1118293/1‑149 (MQ=255)
                                                                                                                         tAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCAtt                   >  2:1222193/1‑149 (MQ=255)
                                                                                                                           aaaTTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAg                                                   <  4:1035997/115‑1 (MQ=255)
                                                                                                                           aaaTTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAg                                                   >  3:1035997/1‑115 (MQ=255)
                                                                                                                            aaTTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTAc                <  1:517032/149‑1 (MQ=255)
                                                                                                                            aaTTAAATCTGTAAGTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTAc                >  2:1018934/1‑149 (MQ=255)
                                                                                                                              ttAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGa              >  3:111792/1‑149 (MQ=255)
                                                                                                                                aaaTCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGAAt            >  3:1236687/1‑149 (MQ=255)
                                                                                                                                  gtCTGTAATAAATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGaa             >  3:188685/2‑146 (MQ=255)
                                                                                                                                  gtCTGTAATAAATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGaa             <  4:188685/145‑1 (MQ=255)
                                                                                                                                   tCTGTAATAAATTACAGTCTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAgg                                          <  2:883627/116‑1 (MQ=255)
                                                                                                                                   tCTGTAATAAATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAgg                                          >  1:883627/1‑116 (MQ=255)
                                                                                                                                    cTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTg                                                             >  3:1350425/1‑96 (MQ=255)
                                                                                                                                    cTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTg                                                             <  4:1350425/96‑1 (MQ=255)
                                                                                                                                     tGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGAttt                                                                   <  1:508199/89‑1 (MQ=255)
                                                                                                                                     tGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGAttt                                                                   >  2:508199/1‑89 (MQ=255)
                                                                                                                                     tGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGa                             >  3:422284/1‑127 (MQ=255)
                                                                                                                                     tGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGa                             <  4:422284/127‑1 (MQ=255)
                                                                                                                                         aTTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGa              >  2:545271/1‑138 (MQ=255)
                                                                                                                                         aTTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGa              <  1:545271/138‑1 (MQ=255)
                                                                                                                                         aTTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGAATGGTTTgaga   >  3:1395118/1‑149 (MQ=255)
                                                                                                                                          tttATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGtt                                                                >  4:538312/1‑87 (MQ=255)
                                                                                                                                          tttATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGtt                                                                <  3:538312/87‑1 (MQ=255)
                                                                                                                                          tttATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGc                                                  >  4:238903/1‑101 (MQ=255)
                                                                                                                                          tttATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGc                                                  <  3:238903/101‑1 (MQ=255)
                                                                                                                                          tttATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGAATGGTTTGAGAt  >  3:1446441/1‑149 (MQ=255)
                                                                                                                                           |                                                                                                                                                   
AAAATTAGTAACACTATTAGACATTTTTAAGGAAACCTCTTTGTTATCTCAATATAAAACTACTATCTGAAATTTCTCAGTGTTGCCCCATTTTTCTCGGGGCAACATCGCTATAAATCAATAAAATTAAATCTGTAATTTATTACAGACTTTCTCGTACAGAAAATGTATCTATAAAATCGAGGACATCTTTACGTAACCAGTAATGGCGGCCATTGATTTGTTTTGGGCGAGGTAGCCCCTCAGGCAATTTGTCCTGACAAAGCCATTTACGAATGGTTTGAGAT  >  NC_000913/294776‑295062

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