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 F1 I2 R1 760 67.6 3323148 92.7% 3080558 109.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,609,336 (C)7→8 intergenic (+13/‑78) yjjG → / → prfC dUMP phosphatase/peptide chain release factor RF‑3

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,609,3291.C98.2% 186.4 / ‑3.6 54intergenic (+6/‑85)yjjG/prfCdUMP phosphatase/peptide chain release factor RF‑3
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (30/23);  total (30/24)
Fisher's exact test for biased strand distribution p-value = 4.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.56e-01

TCGGTGGCATCAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAGCGCCGCACTTTT  >  NC_000913/4609193‑4609461
                                                                                                                                         |                                                                                                                                      
tcGGTGGCATCAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑cc                                                                                                                                     <  1:1477876/139‑1 (MQ=255)
            aCGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGAt                                                                                                                         >  2:5641/1‑139 (MQ=255)
                                    tgAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCg                                                                                                 <  1:5641/139‑1 (MQ=255)
                                        tGCACACCATCGCGTGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGtttt                                                                                             >  2:1327632/1‑139 (MQ=255)
                                             acCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTcaaca                                                                                        >  1:359324/1‑139 (MQ=255)
                                                 tCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAgcg                                                                                    >  1:493564/1‑139 (MQ=255)
                                                  cgcgAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAgcgc                                                                                   >  1:779744/1‑139 (MQ=255)
                                                  cgcgAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAgcgc                                                                                   >  2:3116/1‑139 (MQ=255)
                                                  cgcgAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAgcgc                                                                                   >  1:374350/1‑139 (MQ=255)
                                                          aCCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGAt                                                                           <  2:1361706/139‑1 (MQ=255)
                                                                aGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCt                                                                     <  1:1327632/139‑1 (MQ=255)
                                                                  gCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTa                                                                   <  1:277277/139‑1 (MQ=255)
                                                                    aTCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑ccc‑c                                                                                                                                  >  2:208470/1‑73 (MQ=255)
                                                                    aTCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑ccc‑c                                                                                                                                  >  2:1512834/1‑73 (MQ=255)
                                                                    aTCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑ccc‑c                                                                                                                                  <  1:208470/73‑1 (MQ=255)
                                                                    aTCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑ccc‑c                                                                                                                                  <  1:1512834/73‑1 (MQ=255)
                                                                     tCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACt                                                                 >  1:954171/1‑139 (MQ=255)
                                                                     tCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTc                                                                >  2:432788/1‑139 (MQ=255)
                                                                     tCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTc                                                                >  2:861847/1‑139 (MQ=255)
                                                                     tCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTc                                                                <  1:861847/139‑1 (MQ=255)
                                                                      cgcgCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑ccc‑cccccgttg                                                                                                                          >  1:443870/1‑74 (MQ=255)
                                                                      cgcgCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑ccc‑cccccgttg                                                                                                                          <  2:443870/79‑6 (MQ=255)
                                                                        cgcCCACCTCGACCGTTTCTGCGTTGCTCGATCTGGAGCAGCGCCTGTGTAAACACTGATTGCCT‑‑CCCTCCTCGTTGATCGGTAAAATAGCCGCAATTTTTGGTTTTCAACAAGCGCTGTGCGATGCGGCTTACTGaag                                                             <  2:1367861/139‑1 (MQ=255)
                                                                         gcCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCaa                                                              >  1:973026/1‑137 (MQ=255)
                                                                         gcCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCaa                                                              <  2:973026/137‑1 (MQ=255)
                                                                            cACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAagaaga                                                         <  2:779744/139‑1 (MQ=255)
                                                                            cACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAagaaga                                                         <  2:374350/139‑1 (MQ=255)
                                                                                   aCCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAAtt                                                  >  2:458852/1‑139 (MQ=255)
                                                                                       tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGa                                              >  1:219496/1‑139 (MQ=255)
                                                                                       tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGa                                              >  2:118336/1‑139 (MQ=255)
                                                                                        ttcttcGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCt                                                                                                                                         >  2:450087/1‑49 (MQ=255)
                                                                                        ttcttcGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCt                                                                                                                                         <  1:450087/49‑1 (MQ=255)
                                                                                         tcttcGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACg                                            <  1:432788/139‑1 (MQ=255)
                                                                                                tGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAagaaga                                                         <  1:608072/119‑1 (MQ=255)
                                                                                                tGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAagaaga                                                         >  2:608072/1‑119 (MQ=255)
                                                                                                  cACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAgcgcggcg                                                                               <  2:325463/96‑1 (MQ=255)
                                                                                                  cACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAgcgcggcg                                                                               >  1:325463/1‑96 (MQ=255)
                                                                                                    cGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTa                                 <  1:118336/139‑1 (MQ=255)
                                                                                                    cGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTa                                 <  1:458852/139‑1 (MQ=255)
                                                                                                          ggAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACg                                            >  2:1068591/1‑122 (MQ=255)
                                                                                                          ggAGCAGCTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACg                                            <  1:1068591/122‑1 (MQ=255)
                                                                                                            agcagcTCCTGTGTAAACACTGATTGCCT‑‑ccc‑cccc                                                                                                                               >  1:378152/1‑36 (MQ=255)
                                                                                                            agcagcTCCTGTGTAAACACTGATTGCCT‑‑ccc‑cccc                                                                                                                               <  2:378152/36‑1 (MQ=255)
                                                                                                                 cTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTcc                                    >  1:127870/1‑123 (MQ=255)
                                                                                                                 cTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTcc                                    <  2:127870/123‑1 (MQ=255)
                                                                                                                 cTCCTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTg                    >  1:804126/1‑139 (MQ=255)
                                                                                                                   ccTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGtt                                          >  1:701073/1‑115 (MQ=255)
                                                                                                                   ccTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGtt                                          <  2:701073/115‑1 (MQ=255)
                                                                                                                    cTGTGTAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCg                 <  2:493564/139‑1 (MQ=255)
                                                                                                                       tgtAAACACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAg              >  1:139754/1‑139 (MQ=255)
                                                                                                                           aaCACTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAGcgcc          >  2:450037/1‑139 (MQ=255)
                                                                                                                              acTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTcaa                                                                                          <  2:781319/56‑1 (MQ=255)
                                                                                                                              acTGATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTcaa                                                                                          >  1:781319/1‑56 (MQ=255)
                                                                                                                                 gATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTc                                                                <  1:1427801/79‑1 (MQ=255)
                                                                                                                                 gATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTc                                                                >  2:1427801/1‑79 (MQ=255)
                                                                                                                                 gATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAagaaga                                                         >  1:673984/1‑86 (MQ=255)
                                                                                                                                 gATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAagaaga                                                         <  2:673984/86‑1 (MQ=255)
                                                                                                                                 gATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAagaaga                                                         <  2:508446/86‑1 (MQ=255)
                                                                                                                                 gATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAagaaga                                                         >  1:508446/1‑86 (MQ=255)
                                                                                                                                 gATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGtt                                          <  2:595838/101‑1 (MQ=255)
                                                                                                                                 gATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGtt                                          >  1:595838/1‑101 (MQ=255)
                                                                                                                                 gATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAg              >  1:130619/1‑129 (MQ=255)
                                                                                                                                 gATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAg              <  2:130619/129‑1 (MQ=255)
                                                                                                                                 gATTGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAGCGCCGCACtt    >  2:1612131/1‑139 (MQ=255)
                                                                                                                                   ttGCCTC‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAGCGCCGCACtttt  >  2:1554068/1‑139 (MQ=255)
                                                                                                                                         |                                                                                                                                      
TCGGTGGCATCAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑‑CCC‑CCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAGCGCCGCACTTTT  >  NC_000913/4609193‑4609461

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A