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
A24 F30 I1 R1 17 36.3 1245384 98.8% 1230439 138.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,140,748 C→A A492S (GCC→TCC)  ptsA ← putative PTS multiphosphoryl transfer protein PtsA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,140,7480CA95.7% 150.3 / 0.7 46A492S (GCC→TCC) ptsAputative PTS multiphosphoryl transfer protein PtsA
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base A (25/19);  total (26/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.27e-01

TTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGCGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGAATGTTCAGATAATCAACGGGTTTGTCGCC  >  NC_000913/4140617‑4140874
                                                                                                                                   |                                                                                                                              
tttCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAgcggaggagcggagga                                                                                                                        <  1:292036/140‑1 (MQ=255)
       tcaAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCg                                                                                                                 >  1:134044/1‑140 (MQ=255)
           aCGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGc                                                                                                             >  1:532966/1‑140 (MQ=255)
                 tgtgTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTg                                                                                                       >  2:582333/1‑140 (MQ=255)
                      tCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTaaa                                                                                                  <  1:364589/140‑1 (MQ=255)
                       cGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGCGCGGAGGATCGACCGTAGCTGCg                                                                                                         >  1:174165/1‑132 (MQ=255)
                       cGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGCGCGGAGGATCGACCGTAGCTGCg                                                                                                         <  2:174165/132‑1 (MQ=255)
                             gTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAacgac                                                                                           >  1:563940/1‑140 (MQ=255)
                             gTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAacgac                                                                                           >  1:490675/1‑140 (MQ=255)
                                gTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGAcgcg                                                                                        <  2:321428/140‑1 (MQ=255)
                                 ttGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGt                                                                                       >  2:253840/1‑140 (MQ=255)
                                  tGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTa                                                                                      <  2:563940/140‑1 (MQ=255)
                                  tGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTa                                                                                      <  1:209307/140‑1 (MQ=255)
                                   gCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTAc                                                                                     >  1:449312/1‑140 (MQ=255)
                                       tttGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCtt                                                                                 <  2:140232/140‑1 (MQ=255)
                                       tttGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCtt                                                                                 >  1:140232/1‑140 (MQ=255)
                                                 gCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACg                                                                       <  2:449312/140‑1 (MQ=255)
                                                 gCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACg                                                                       >  1:72230/1‑140 (MQ=255)
                                                    aGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCAc                                                                    <  1:546659/140‑1 (MQ=255)
                                                    aGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCAc                                                                    <  2:134044/140‑1 (MQ=255)
                                                                aCCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAAcc                                                        >  1:78900/1‑140 (MQ=255)
                                                                aCCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAAcc                                                        >  2:47300/1‑140 (MQ=255)
                                                                     tAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGa                                                   <  1:253840/140‑1 (MQ=255)
                                                                            tctTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGa                                                   >  1:587868/1‑133 (MQ=255)
                                                                            tctTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGa                                                   <  2:587868/133‑1 (MQ=255)
                                                                            tctTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGtt                                            >  1:388879/1‑140 (MQ=255)
                                                                            tctTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGtt                                            >  1:431498/1‑140 (MQ=255)
                                                                              ttCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTg                                          >  1:129837/1‑140 (MQ=255)
                                                                               tCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGc                                         <  2:207985/140‑1 (MQ=255)
                                                                                      aggagATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCg                                  >  2:473759/1‑140 (MQ=255)
                                                                                        gagaTCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCTTCTGCggg                                <  1:582333/140‑1 (MQ=255)
                                                                                        gagaTCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCggg                                >  1:283963/1‑140 (MQ=255)
                                                                                         agaTCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGa                               <  2:72230/140‑1 (MQ=255)
                                                                                         agaTCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGa                               <  2:532966/140‑1 (MQ=255)
                                                                                          gaTCATCGGGATCACGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGaa                              <  2:163227/140‑1 (MQ=255)
                                                                                             catcGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGc                                         >  1:552215/1‑126 (MQ=255)
                                                                                             catcGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGc                                         <  2:552215/126‑1 (MQ=255)
                                                                                             catcGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGAATGt                           >  1:322838/1‑140 (MQ=255)
                                                                                                cGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGa                               >  2:99370/1‑133 (MQ=255)
                                                                                                cGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGa                               <  1:99370/133‑1 (MQ=255)
                                                                                                cGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGAATGTTCa                        >  2:175295/1‑140 (MQ=255)
                                                                                                          aTTTTCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGAATGTTCAGATAATCAAc              <  2:78900/140‑1 (MQ=255)
                                                                                                              tCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGAATGTTCAGATAATCAACGGGt          <  2:129837/140‑1 (MQ=255)
                                                                                                              tCAGGCTGCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGAATGTTCAGATAATCAACGGGt          >  2:73394/1‑140 (MQ=255)
                                                                                                                     gCCGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGAATGTTCAGATAATCAACGGGTTTGTcgc   >  2:412336/1‑140 (MQ=255)
                                                                                                                      ccGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGAATGTTCAGATAATCAACGGGTTTGTcgcc  >  1:274169/1‑140 (MQ=255)
                                                                                                                      ccGTGAGCGGAGGAGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGAATGTTCAGATAATCAACGGGTTTGTcgcc  >  1:413960/1‑140 (MQ=255)
                                                                                                                                   |                                                                                                                              
TTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCCGTGAGCGGAGGCGCGGAGGATCGACCGTAGCTGCGTGGTAAACAACGACGCGTACTCTTCATAAATACGCACGGCGCGATAACCGAGGAACGGGTTTGCCTCTGCGGGAATGTTCAGATAATCAACGGGTTTGTCGCC  >  NC_000913/4140617‑4140874

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A