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
A34 F5 I0 R1 408 67.6 2494072 96.8% 2414261 139.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,517,481 C→G 7.4% R31R (CGC→CGG)  ydcX → DUF2566 family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,517,4810CG 7.4% 184.3 / 4.2 53R31R (CGC→CGG) ydcXDUF2566 family protein
Reads supporting (aligned to +/- strand):  ref base C (24/25);  new base G (2/2);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01

AAAAATGACGCATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCAC  >  NC_000913/1517337‑1517628
                                                                                                                                                |                                                                                                                                                   
aaaaaTGACGCATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATcc                                                                                                                                                 >  3:546279/1‑149 (MQ=255)
aaaaaTGACGCATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATcc                                                                                                                                                 >  2:597727/1‑149 (MQ=255)
  aaaTGACGCATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGt                                                                                                                                               <  4:608863/149‑1 (MQ=255)
    aTGACGCATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGttt                                                                                                                                             <  1:597727/149‑1 (MQ=255)
                   gcgcgTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCt                                                                                                                              <  1:188883/149‑1 (MQ=255)
                   gcgcgTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCt                                                                                                                              <  1:420395/149‑1 (MQ=255)
                   gcgcgTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGGTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCt                                                                                                                              >  3:146644/1‑149 (MQ=255)
                        ttttATTCATCTGGCTGGACGCCCATACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGGATGCGTTTCTTatc                                                                                                                                       <  3:373967/135‑3 (MQ=255)
                        ttttATTCATCTGGCTGGACGCCCATACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGGATGCGTTTCTTatc                                                                                                                                       >  4:373967/1‑133 (MQ=255)
                          ttATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTgggg                                                                                                                       <  1:164682/149‑1 (MQ=255)
                                   tggctggACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATgg                                                                                                              >  1:5473/1‑149 (MQ=255)
                                    ggctggACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGc                                                                                                             <  4:72506/149‑1 (MQ=255)
                                         gACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATg                                                                                                        >  3:152735/1‑149 (MQ=255)
                                          aCGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGa                                                                                                       <  3:357969/149‑1 (MQ=255)
                                           cGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAg                                                                                                      <  4:32210/149‑1 (MQ=255)
                                              ccGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAgc                                                                                                                                      >  3:69363/1‑114 (MQ=255)
                                              ccGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAgc                                                                                                                                      <  4:69363/114‑1 (MQ=255)
                                                  aCATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCg                                                                                               >  1:291906/1‑149 (MQ=255)
                                                      gTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCt                                                                                                                              <  1:330792/114‑1 (MQ=255)
                                                      gTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCt                                                                                                                              >  2:330792/1‑114 (MQ=255)
                                                      gTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTccc                                                                                                <  1:94924/144‑1 (MQ=255)
                                                      gTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTccc                                                                                                >  2:94924/1‑144 (MQ=255)
                                                         tctctATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGgcgc                                                                                        >  1:185941/1‑149 (MQ=255)
                                                         tctctATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGgcgc                                                                                        >  3:492274/1‑149 (MQ=255)
                                                             tATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCtgtt                                                                                    <  2:5473/149‑1 (MQ=255)
                                                                  acacATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCtggtgg                                                                                                                         >  1:208224/1‑107 (MQ=255)
                                                                  acacATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCtggtgg                                                                                                                         <  2:208224/107‑1 (MQ=255)
                                                                  acacATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGtttt                                                                               >  2:89100/1‑149 (MQ=255)
                                                                   cacaTGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTc                                                                              <  1:520380/149‑1 (MQ=255)
                                                                    acaTGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCa                                                                             <  2:257428/149‑1 (MQ=255)
                                                                         cTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGtt                                                                        >  4:364480/1‑149 (MQ=255)
                                                                          ttGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGttt                                                                       <  4:290001/149‑1 (MQ=255)
                                                                          ttGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGttt                                                                       >  2:237650/1‑149 (MQ=255)
                                                                               ttttATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAAt                                                                  <  1:237650/149‑1 (MQ=255)
                                                                                              gcagcaATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCtt                                                   >  2:136996/1‑149 (MQ=255)
                                                                                                    aTCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTAc                                                             <  4:499804/133‑1 (MQ=255)
                                                                                                    aTCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTAc                                                             >  3:499804/1‑133 (MQ=255)
                                                                                                     tCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGca                                            <  4:146644/149‑1 (MQ=255)
                                                                                                       gCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGcacc                                          >  4:312403/1‑149 (MQ=255)
                                                                                                                  cACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTta                               <  1:89100/149‑1 (MQ=255)
                                                                                                                             tttctCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACtt                                <  2:461878/137‑1 (MQ=255)
                                                                                                                             tttctCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGa                    >  1:563280/1‑149 (MQ=255)
                                                                                                                             tttctCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGa                    >  1:494551/1‑149 (MQ=255)
                                                                                                                             tttctCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACAGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACtt                                >  1:461878/1‑137 (MQ=255)
                                                                                                                              ttctCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGAt                   <  1:377732/149‑1 (MQ=255)
                                                                                                                                 tcACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGca                                            <  2:497309/121‑1 (MQ=255)
                                                                                                                                 tcACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGca                                            >  1:497309/1‑121 (MQ=255)
                                                                                                                                 tcACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGaa                <  1:136996/149‑1 (MQ=255)
                                                                                                                                   aCGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATc              >  4:358911/1‑149 (MQ=255)
                                                                                                                                      ttAAGAAACGGATGCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCAttt                       <  2:146963/136‑1 (MQ=255)
                                                                                                                                      ttAAGAAACGGATGCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCAttt                       >  1:146963/2‑137 (MQ=255)
                                                                                                                                               gCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTcac  >  3:271796/1‑149 (MQ=255)
                                                                                                                                               gCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTcac  <  4:492274/149‑1 (MQ=255)
                                                                                                                                                |                                                                                                                                                   
AAAAATGACGCATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCAC  >  NC_000913/1517337‑1517628

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