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
A5 F28 I1 R1 260 73.5 2514320 99.3% 2496719 138.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,822,554 T→C V52A (GTT→GCT)  spoT → bifunctional (p)ppGpp synthase/hydrolase SpoT

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,822,5540TC98.1% 179.7 / ‑5.0 53V52A (GTT→GCT) spoTbifunctional (p)ppGpp synthase/hydrolase SpoT
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (27/25);  total (28/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TGAATCAACTGATTCAAACCTACCTGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGTTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAACAGCTTTTTGGTAAAAGCGTCGCCGAGC  >  NC_000913/3822419‑3822685
                                                                                                                                       |                                                                                                                                   
tGAATCAACTGATTCAAACCTACCTGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGcc                                                                                                                                 <  2:343693/140‑1 (MQ=255)
        cTGATTCAAACCTACCTGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCt                                                                                                                         >  1:321920/1‑140 (MQ=255)
            ttCAAACCTACCTGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGcc                                                                                                                     <  2:296788/140‑1 (MQ=255)
              cAAACCTACCTGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCga                                                                                                                   >  2:113510/1‑140 (MQ=255)
              cAAACCTACCTGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCga                                                                                                                   >  2:488009/1‑140 (MQ=255)
                     acctGCCGGAAGACCAGATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGaaa                                                                                                            >  1:763101/1‑140 (MQ=255)
                     acctGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCTTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGaaa                                                                                                            >  1:614873/1‑140 (MQ=255)
                      cctGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGcc                                                                                                                     <  2:1126569/130‑1 (MQ=255)
                      cctGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGcc                                                                                                                     >  1:1126569/1‑130 (MQ=255)
                      cctGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAAc                                                                                                           >  1:496853/1‑140 (MQ=255)
                       ctGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACt                                                                                                          <  2:321920/140‑1 (MQ=255)
                       ctGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACt                                                                                                          <  1:927262/140‑1 (MQ=255)
                          ccGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGa                                                                                                       >  2:1010533/1‑140 (MQ=255)
                           cGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGa                                                                                                              >  1:381728/1‑132 (MQ=255)
                           cGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGa                                                                                                              <  2:381728/132‑1 (MQ=255)
                             gAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTa                                                                                                    >  2:1200602/1‑140 (MQ=255)
                                gACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGa                                                                                                 <  2:1151796/140‑1 (MQ=255)
                                              tCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATggcgg                                                                                   <  1:1010533/140‑1 (MQ=255)
                                               cTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATggcggc                                                                                  >  2:525827/1‑140 (MQ=255)
                                                tGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGgcggcg                                                                                 <  2:496853/140‑1 (MQ=255)
                                                tGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGgcggcg                                                                                 >  2:560440/1‑140 (MQ=255)
                                                    gCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCgctgc                                                                             <  2:87778/140‑1 (MQ=255)
                                                                 gTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGAt                                                                <  1:788676/140‑1 (MQ=255)
                                                                       ggTGATGCTCACGGGGGGCAAACACGTTCAGGCGGTGACCCCTATACCCCGCCCCCGGTAGCGGCTGCCTGCATTCGGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGa                                                          <  2:971672/139‑1 (MQ=255)
                                                                       cGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGTTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATg                                                                       >  1:738899/1‑127 (MQ=255)
                                                                       cGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGTTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATg                                                                       <  2:738899/127‑1 (MQ=255)
                                                                          gATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATAc                                                       >  2:1191523/1‑140 (MQ=255)
                                                                           aTGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACg                                                                    >  1:722307/1‑126 (MQ=255)
                                                                           aTGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACg                                                                    <  2:722307/126‑1 (MQ=255)
                                                                                 aCGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGcc                                                <  2:651039/140‑1 (MQ=255)
                                                                                  cGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCa                                               <  2:334110/140‑1 (MQ=255)
                                                                                  cGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCa                                               <  2:906759/140‑1 (MQ=255)
                                                                                    aGGGGCAAGCTCGTTCAAGCGGTAAGATCTATATCTCGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAGCTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCcccc                                             <  2:551021/140‑1 (MQ=255)
                                                                                    aGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCAcc                                             <  2:763101/140‑1 (MQ=255)
                                                                                      gggCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTa                                           <  2:1038340/140‑1 (MQ=255)
                                                                                        gCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTAcc                                         <  1:560440/140‑1 (MQ=255)
                                                                                        gCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTAcc                                         >  2:363668/1‑140 (MQ=255)
                                                                                        gCAAACACGTTCAAGCGGTGAACCATATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTAcc                                         >  2:156989/1‑140 (MQ=255)
                                                                                         cAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCa                                        <  2:614873/140‑1 (MQ=255)
                                                                                           aaCACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAgg                                      >  2:849947/1‑140 (MQ=255)
                                                                                            acacGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGTTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGa                                     <  2:406196/140‑1 (MQ=255)
                                                                                                 ttCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATgg                                >  2:275906/1‑140 (MQ=255)
                                                                                                   cAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGag                              <  1:1200602/140‑2 (MQ=255)
                                                                                                          tGAACCCTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCttt                       <  1:363668/140‑1 (MQ=255)
                                                                                                                cTATATCACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTa                 >  2:530531/1‑140 (MQ=255)
                                                                                                                      cACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCg           >  1:699914/1‑140 (MQ=255)
                                                                                                                      cACGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCg           >  1:1162455/1‑140 (MQ=255)
                                                                                                                        cGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTc         >  1:1244519/1‑140 (MQ=255)
                                                                                                                        cGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTc         >  1:179434/1‑140 (MQ=255)
                                                                                                                        cGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTc         >  1:508173/1‑140 (MQ=255)
                                                                                                                        cGCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTc         >  1:558550/1‑140 (MQ=255)
                                                                                                                         gCACCCGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCg        >  2:370235/1‑140 (MQ=255)
                                                                                                                            cccGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCg     <  1:385865/140‑1 (MQ=255)
                                                                                                                            cccGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCg     <  1:1191523/140‑1 (MQ=255)
                                                                                                                              cGGTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAg   <  2:1162455/140‑1 (MQ=255)
                                                                                                                               ggTAGCGGCTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAGCAGCTTTTTGGTAAAAGCGTCGCCGAGc  >  2:738876/1‑140 (MQ=255)
                                                                                                                                       |                                                                                                                                   
TGAATCAACTGATTCAAACCTACCTGCCGGAAGACCAAATCAAGCGTCTGCGGCAGGCGTATCTCGTTGCACGTGATGCTCACGAGGGGCAAACACGTTCAAGCGGTGAACCCTATATCACGCACCCGGTAGCGGTTGCCTGCATTCTGGCCGAGATGAAACTCGACTATGAAACGCTGATGGCGGCGCTGCTGCATGACGTGATTGAAGATACTCCCGCCACCTACCAGGATATGGAACAGCTTTTTGGTAAAAGCGTCGCCGAGC  >  NC_000913/3822419‑3822685

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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