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
A7 F97 I2 R1 17 63.6 2309030 90.9% 2098908 142.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,019,729 C→T P190L (CCG→CTG)  ssnA → putative chlorohydrolase/aminohydrolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,019,7290CT98.0% 142.4 / NA 50P190L (CCG→CTG) ssnAputative chlorohydrolase/aminohydrolase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (26/22);  minor base G (0/1);  total (27/23)
Fisher's exact test for biased strand distribution p-value = 4.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

TTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCCGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCACAGGCCGTGGTTTGCATATTCACGCTGCGGAAGACCTTTACGACGTT  >  NC_000913/3019589‑3019865
                                                                                                                                            |                                                                                                                                        
tttCAAAGTTCGCCTGCGCGCGATGACCTGTTTTGAAACTACTGGCCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGt                                                                                                                                        <  2:253352/143‑1 (MQ=255)
 ttAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTCACAACGGCATCAAAGAGTTGCAGGCAGGTGTAGAAGGAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTa                                                                                                                                       >  1:1008921/1‑143 (MQ=255)
       gtgggCCTGCGGGCGATGACCTGTTTTGAAACTGGTGACCGTGACAACGGCATCAAAGAGTTGGAGGAAGGGGTAGGAGAAAACAGCCGTGTCGCGCGTTTGAGTGAGGAGGCGAAGAAAGCGACAAGCGAGCTGTATCtggt                                                                                                                                 <  2:194979/140‑1 (MQ=255)
       gTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGCAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCtggt                                                                                                                                 <  1:513802/143‑1 (MQ=255)
            ccTGCGCGCGATGACCTGTGTGGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAg                                                                                                                            <  2:1014475/143‑1 (MQ=255)
              tGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGca                                                                                                                          >  1:428400/1‑143 (MQ=255)
                     gATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAGGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCg                                                                                                                   >  1:12596/1‑143 (MQ=255)
                      aTGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCgg                                                                                                                  <  1:1115878/143‑1 (MQ=255)
                           cTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGAAAAGCGAGCTGGACCTGGTGGAAGCAAATACCGGtacgc                                                                                                             >  2:283276/1‑139 (MQ=255)
                                   aaaCTACTGACCGTAACAACGGCATCAAAGAGGTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCg                                                                                                     >  1:804108/1‑143 (MQ=255)
                                    aaCTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTAGCTGGCGGAAGCACATACCCGTGCTCACccgccga                                                                                                    >  2:153398/1‑142 (MQ=255)
                                       tactGACCGTAACAACGGCATCAAAGAGTTGCAGGCAGGTGTACGAGAAAACATCCGTTTCGCCCGCTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCAGCAACTGGTGGAAGCACATAACGGTGCTCACGCGCCGTTTa                                                                                                 >  2:70460/1‑143 (MQ=255)
                                           gACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCAGACATCGGTGCGCACGCGCCGGTGACCGt                                                                                             >  2:27083/1‑143 (MQ=255)
                                           gACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTAccat                                                                                             <  1:455767/143‑3 (MQ=255)
                                            aCCGTAACAACGGCATCACAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGGTTACCGTg                                                                                            >  1:1023247/1‑143 (MQ=255)
                                            aCCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGCGGCTCCGACAGCGACAAGCCACCTGTATCTGGTGGACACACATAACGGTGCTCACTCGCCGTCTACCGta                                                                                            >  1:371524/1‑142 (MQ=255)
                                              cGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGAACATATCGGTGCTAACGGGACGTTTagagtgta                                                                                          >  2:422329/1‑136 (MQ=255)
                                                 aacaacGGCCTCGAAGGGTGGCTGGACGGTGTAGAAGAAAGCATCCCTTTCGGCCGTTTGATTGGTTAGGAGAAGAAATCGACAAGCGAGCTGTATCTGGTGTAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGa                                                                                       <  2:61028/143‑1 (MQ=255)
                                                          accAAAGCGTCGCAGGAAGGTGTACCAGAAAACATCCGTTCCGCCCGTTTGATTGCTGAGGCGAAGACAGCGACAAGCGCGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCt                                                                              <  1:248644/141‑1 (MQ=255)
                                                          aTCAGAGGGTTGGAGGAAGGGGGAGAAGAAAACATCCGTGTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCt                                                                              <  2:559234/143‑1 (MQ=255)
                                                          aTCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAGGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCAGATATGGGTGCTCACGCGGCGCTTACCGTGCCGGATGCCgggcg                                                                              >  1:506908/1‑140 (MQ=255)
                                                           tCAAAGATTTGCAGGAAGGTGTAGAAGAAAACATCCGTGTCGCCCGTTTGATTGATGGGGCGACGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTg                                                                             <  2:374137/143‑1 (MQ=255)
                                                           tCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCACCGTTTACCGTGCCGGATGCCGGTCTg                                                                             >  1:660245/1‑143 (MQ=255)
                                                              aaGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGCTGCCGGCCTGgag                                                                          >  2:424112/1‑143 (MQ=255)
                                                                   ttGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGCTTGATGAGGCGCAGAAAGCGACAAGCGAGCTGTATCTGGTTGAACCACATATCGGTGCTCACTCTCCGTTTCCCGCTCCGGATGCCGGTGTGGGGGtgct                                                                     >  1:130130/1‑143 (MQ=255)
                                                                     gCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCGCGTTTGATTGCTGAGGCGAAGAAAGCGACAAGGGCGCTGTACCTGGCGGCAGCACATATCGGAGACCACGCGCGGTTTACGCTGCAGGATGCAGGAGTCGAGAtggtgc                                                                   >  2:561413/1‑143 (MQ=255)
                                                                       attgatgtgtAGAAGAAAACATCCGTGTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGt                                                                 <  1:522458/137‑1 (MQ=255)
                                                                           aGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAg                                                             <  1:153530/143‑1 (MQ=255)
                                                                             gtgtAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCCTGCCGGAGCCCGGTCTGGAGATGCTGCGTGAAgtc                                                           >  2:910164/1‑141 (MQ=255)
                                                                               gtAGAAGAAGCCGTCCGTTGCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGt                                                         <  2:550841/143‑1 (MQ=255)
                                                                                tAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGTATGCCGGACGGGAGATGCTGCGTGCAGCCGtc                                                        >  2:896235/1‑142 (MQ=255)
                                                                                tAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTg                                                        >  1:126597/1‑143 (MQ=255)
                                                                                  gaagacACCATCCGTGTGGCTCGTTTGATTGATGAGGTGAAGAACGCGACAAGCGAGCTGTATCTGGGGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGaa                                                      <  2:118161/143‑1 (MQ=255)
                                                                                   aagaaAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGCTGCTACGTGAGGCAGTGaaa                                                     >  2:318342/1‑143 (MQ=255)
                                                                                    agaagaCATCCGTTTGGCCCGTTTTATTGAGGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCATGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGAGTGAAGCCGTGaatg                                                    <  2:825429/143‑3 (MQ=255)
                                                                                             ccGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCACAGGcc                                           >  1:1022199/1‑143 (MQ=255)
                                                                                                 ttCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCACAGGCCGTgg                                       <  1:102612/143‑1 (MQ=255)
                                                                                                       ggtctgatggagGGGGCGAAGAAAGCGACAAGCGAGCGGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGGTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCACAGGCCGTGGTTTGCa                                 <  2:392130/139‑1 (MQ=255)
                                                                                                         tttGATTGATGAGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCAGGCGCCGTTTACCGTGCCGGATGCGGGGCTGGAGATGCTGCGTGAGGCCGTGAAAGCGACAGGCCGGGGtgggcgta                               >  1:347836/1‑136 (MQ=255)
                                                                                                               tgatgaGGCGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCACAGGCCGTGGTTTGCATATTcgcg                         >  1:638255/1‑143 (MQ=255)
                                                                                                                      gCGAAGAAAGCGACAAGCGAGCTGTCTCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAGAGCCACAGGCCGTGCTTTGCACATCCACGCTGCGGa                  >  2:78554/1‑143 (MQ=255)
                                                                                                                       cGAAGAAAGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCACAGGCCGTGGTTGGCATATTCACGCTGCGGaa                 >  1:976329/1‑143 (MQ=255)
                                                                                                                          agaagccgacgaGCGGGCTGCATCGGGTGGAAGCACAGATCGGTGCTCACGCGCCGTGTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCACAGGCCGTGGTTTGCATATTCACGCTGCGGAAGAc              <  2:946247/137‑1 (MQ=255)
                                                                                                                            aaaGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCACAGGCCGTGGTTTGCATATTCACGCTGCGGAAGACCt            <  1:1122392/143‑1 (MQ=255)
                                                                                                                             aaGCGCCAAGCGAGCTGTATCTGGTGGACGCACCTATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCACAGGCCGTGGTTTGCATATTCACGCTGCGGAAGACCtt           <  1:657038/143‑1 (MQ=255)
                                                                                                                             aaGCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCACAGGCCGTGGTTTGCATATTCACGCTGCGGAAGACCtt           <  2:428400/143‑1 (MQ=255)
                                                                                                                               gCGACAAGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCACAGGCCGTGGTTTGCATATTCACGCTGCGGAAGACCTTTa         <  1:1076010/143‑1 (MQ=255)
                                                                                                                                   cAAGCGAGCTGTATCTGGTGGAAGCAGATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCACAGGCCGTGGTTTGCATATTCACGCTGCGGAAGACCTTTacgac     <  1:649836/143‑1 (MQ=255)
                                                                                                                                    aaGCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCCCAGGACGTGGTTTGCACCTTCACGCTGCGGAAGCCCTTTacgacg    >  1:441925/1‑143 (MQ=255)
                                                                                                                                      gCGAGCTGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCACAGGCCGTGGTTTGCATATTCACGCTGCGGAAGACCTTTACGACGtt  >  1:736618/1‑143 (MQ=255)
                                                                                                                                            |                                                                                                                                        
TTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCCGTATCTGGTGGAAGCACATATCGGTGCTCACGCGCCGTTTACCGTGCCGGATGCCGGTCTGGAGATGCTGCGTGAAGCCGTGAAAGCCACAGGCCGTGGTTTGCATATTCACGCTGCGGAAGACCTTTACGACGTT  >  NC_000913/3019589‑3019865

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A