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
A11 F28 I1 R1 224 87.5 2960670 99.3% 2939945 138.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,786,297 T→C G346G (GGT→GGC)  gpmM → 2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,786,2970TC100.0% 185.7 / NA 54G346G (GGT→GGC) gpmM2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (29/25);  total (29/25)

ATCAAAACTGCGGTTGCTTACCCACCCGCTTCCCTGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGTGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGAAAAACTGGTTGCGGCCATCAAGAGCGGCAAAT  >  NC_000913/3786163‑3786433
                                                                                                                                      |                                                                                                                                        
aTCAAAACTGCGGTTGCTTACCCACCCGCTTCCCTGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGt                                                                                                                                     >  2:78719/1‑140 (MQ=255)
     aaCTGCGGTTGCTTACCCACCCGCTTCCCTGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTagaag                                                                                                                                >  1:1303045/1‑140 (MQ=255)
       cTGCGGTTGCTTACCCACCCGCTTCCCTGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAagag                                                                                                                              <  1:101596/140‑1 (MQ=255)
          cGGTTGCTTACCCACCCGCTTCCCTGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCg                                                                                                                           >  1:896737/1‑140 (MQ=255)
                     ccacccGCTTCCCTGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGa                                                                                                                <  1:1123027/140‑1 (MQ=255)
                       acccGCTTCCCTGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAg                                                                                                              >  2:284704/1‑140 (MQ=255)
                         ccGCTTCCCTGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGAt                                                                                                            >  2:230372/1‑140 (MQ=255)
                         ccGCTTCCCTGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGAt                                                                                                            >  1:273211/1‑140 (MQ=255)
                          cGCTTCCCTGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATc                                                                                                           <  2:1285738/140‑1 (MQ=255)
                          cGCTTCCCTGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATc                                                                                                           <  1:71332/140‑1 (MQ=255)
                           gCTTCCCTGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCg                                                                                                          >  1:888964/1‑140 (MQ=255)
                           gCTTCCCTGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCg                                                                                                          >  1:422007/1‑140 (MQ=255)
                                  tGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTg                                                                                                   >  1:1455381/1‑140 (MQ=255)
                                  tGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTg                                                                                                   >  1:262431/1‑140 (MQ=255)
                                    gTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGAt                                                                                                 <  2:226597/140‑1 (MQ=255)
                                     ttAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATc                                                                                                <  2:422007/140‑1 (MQ=255)
                                     ttAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATc                                                                                                <  2:273211/140‑1 (MQ=255)
                                     ttAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATc                                                                                                <  2:888964/140‑1 (MQ=255)
                                         cacCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACt                                                                                            >  2:86985/1‑140 (MQ=255)
                                           ccTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCa                                                                                          <  2:564136/140‑1 (MQ=255)
                                           ccTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCa                                                                                          >  1:10987/1‑140 (MQ=255)
                                              tCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCg                                                                                       >  1:1405259/1‑140 (MQ=255)
                                                  cGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAg                                                                                   <  1:39377/140‑1 (MQ=255)
                                                  cGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAg                                                                                   <  2:879756/140‑1 (MQ=255)
                                                     gTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTgg                                                                                <  2:1455381/140‑1 (MQ=255)
                                                     gTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTgg                                                                                <  2:896737/140‑1 (MQ=255)
                                                     gTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTgg                                                                                <  2:341896/140‑1 (MQ=255)
                                                     gTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTgg                                                                                <  2:1303045/140‑1 (MQ=255)
                                                      tGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGc                                                                               <  2:143357/140‑1 (MQ=255)
                                                        gATGGCGAAAAACGACAAAACTCAGTTGCATATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGcta                                                                             >  2:1417505/1‑140 (MQ=255)
                                                            gCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGctaccta                                                                         <  2:262431/140‑1 (MQ=255)
                                                                aaaaCGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGc                                                                               >  2:551571/1‑130 (MQ=255)
                                                                aaaaCGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGc                                                                               <  1:551571/130‑1 (MQ=255)
                                                                         aaaCTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCg                                                            <  1:230372/140‑1 (MQ=255)
                                                                                    cGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTc                                                 >  1:1458662/1‑140 (MQ=255)
                                                                                      tATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGTAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCg                                               >  1:874987/1‑140 (MQ=255)
                                                                                        tttCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCa                                             <  2:1458662/140‑1 (MQ=255)
                                                                                              aaaccgaaaAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAg                                                    >  2:923332/1‑127 (MQ=255)
                                                                                              aaaccgaaaAATATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAg                                                    <  1:923332/127‑1 (MQ=255)
                                                                                                    aaaaaTATGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGaa                                 >  1:1185757/1‑140 (MQ=255)
                                                                                                           tGCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCATAGCTGACCGAAAAACTgg                          >  1:374416/1‑140 (MQ=255)
                                                                                                            gCCCACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGAAAAACTGGt                         >  2:834753/1‑140 (MQ=255)
                                                                                                              ccACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGAAAAACTGGTTg                       <  2:903958/140‑1 (MQ=255)
                                                                                                               cACGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTAACCGAAAAACTGGTTGc                      >  1:779686/1‑140 (MQ=255)
                                                                                                                aCGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGAAAAACTGGTTGCg                     <  1:1417505/140‑1 (MQ=255)
                                                                                                                 cGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGAAAAACTGGTTGCgg                    >  1:1212517/1‑140 (MQ=255)
                                                                                                                 cGTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTAACCGAAAAACTGGTTGCgg                    <  2:779686/140‑1 (MQ=255)
                                                                                                                  gTTACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGTCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGAAAAACTGGTTGCGGc                   >  2:816048/1‑140 (MQ=255)
                                                                                                                   ttACTTTCTTCTTCAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGAAAAACTGGTTGCGGcc                  >  1:891422/1‑140 (MQ=255)
                                                                                                                            tcttcAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGAAAAACTGGTTGCGGCCATCAAGAGc         >  1:331350/1‑140 (MQ=255)
                                                                                                                              ttcAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGAAAAACTGGTTGCGGCCATCAAGAGCgg       >  1:239658/1‑140 (MQ=255)
                                                                                                                                cAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGAAAAACTGGTTGCGGCCATCAag            <  2:673676/133‑1 (MQ=255)
                                                                                                                                cAACGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGAAAAACTGGTTGCGGCCATCAag            >  1:673676/1‑133 (MQ=255)
                                                                                                                                 aaCGGCGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGAAAAACTGGTTGCGGCCATCAAGAGCGGCaa    >  1:215878/1‑140 (MQ=255)
                                                                                                                                   cggcggCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGAAAAACTGGTTGAGGCCATCAAGAGCGGCaaaa  >  1:1127330/1‑139 (MQ=255)
                                                                                                                                      |                                                                                                                                        
ATCAAAACTGCGGTTGCTTACCCACCCGCTTCCCTGGTTAACACCTTCGGCGAGTGGATGGCGAAAAACGACAAAACTCAGTTGCGTATTTCCGAAACCGAAAAATATGCCCACGTTACTTTCTTCTTCAACGGTGGCGTAGAAGAGTCGTTCAAAGGCGAAGATCGCATTCTGATCAACTCACCGAAAGTGGCTACCTACGATCTGCAACCGGAAATGAGCTCCGCAGAGCTGACCGAAAAACTGGTTGCGGCCATCAAGAGCGGCAAAT  >  NC_000913/3786163‑3786433

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