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
A6 F1 I2 R1 758 59.3 2864096 93.9% 2689386 105.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,101,039 (C)7→8 coding (585/720 nt) yggN ← DUF2884 family putative periplasmic protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,101,0321.C98.0% 172.9 / ‑3.4 50coding (592/720 nt)yggNDUF2884 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (22/27);  total (23/27)
Fisher's exact test for biased strand distribution p-value = 4.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.11e-01

AAATAGAGGATTATTTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGATTCACTAATTGCTGGCCTTCGGCG  >  NC_000913/3100894‑3101165
                                                                                                                                           |                                                                                                                                       
aaaTAGAGGATTATTTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAg                                                                                                                                          <  1:1337189/139‑1 (MQ=255)
 aaTAGAGGATTATTTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑c                                                                                                                                       <  2:726499/139‑1 (MQ=255)
     gagGATTATTTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑c                                                                                                                                       <  2:1368804/135‑1 (MQ=255)
     gagGATTATTTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑c                                                                                                                                       >  1:1368804/1‑135 (MQ=255)
      agGATTATTTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑accccc                                                                                                                                  <  2:915689/139‑1 (MQ=255)
         attattTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑cccccccca                                                                                                                               <  1:1141723/139‑3 (MQ=255)
                 aaaTTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTccc                                                                                                                       <  2:1311316/139‑1 (MQ=255)
                  aaTTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCa                                                                                                                      <  1:1276323/139‑1 (MQ=255)
                  aaTTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCa                                                                                                                      <  2:760231/139‑1 (MQ=255)
                    ttCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGc                                                                                                                    <  1:1251995/139‑1 (MQ=255)
                       ccGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGcaca                                                                                                                 >  2:559571/1‑139 (MQ=255)
                       ccGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGcaca                                                                                                                 >  1:1175723/1‑139 (MQ=255)
                         gACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACAtt                                                                                                               <  2:599256/139‑1 (MQ=255)
                         gACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACAtt                                                                                                               <  1:486710/139‑1 (MQ=255)
                                   ttGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATggg                                                                                                     >  1:815497/1‑139 (MQ=255)
                                            tCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTAccgccg                                                                                            <  1:1165854/139‑1 (MQ=255)
                                            tCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTAccgccg                                                                                            <  2:815497/139‑1 (MQ=255)
                                                      tCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTccc                                                                                                                       <  1:1057073/102‑1 (MQ=255)
                                                      tCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTccc                                                                                                                       >  2:1057073/1‑102 (MQ=255)
                                                      tCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGcac                                                                                                                  >  1:1158345/1‑107 (MQ=255)
                                                      tCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGcac                                                                                                                  <  2:1158345/107‑1 (MQ=255)
                                                      tCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCa                                                                                  >  2:698224/1‑139 (MQ=255)
                                                      tCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCa                                                                                  >  1:1146877/1‑139 (MQ=255)
                                                        acaACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCAc                                                                                 >  1:1163514/1‑138 (MQ=255)
                                                        acaACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCAc                                                                                 <  2:1163514/138‑1 (MQ=255)
                                                          aaCGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑ccccccccca                                                                                                                              <  1:383234/91‑4 (MQ=255)
                                                          aaCGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑ccccccccca                                                                                                                              >  2:383234/1‑88 (MQ=255)
                                                                gCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTcgc                                                                        >  1:187845/1‑139 (MQ=255)
                                                                 cTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTcgcg                                                                       <  2:950755/139‑1 (MQ=255)
                                                                        cATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAttt                                                                <  2:187845/139‑1 (MQ=255)
                                                                              tGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGca                                                                                                                   <  2:862996/82‑1 (MQ=255)
                                                                              tGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGca                                                                                                                   >  1:862996/1‑82 (MQ=255)
                                                                                ccAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATg                                                        <  2:447292/139‑1 (MQ=255)
                                                                                     ctgctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt                                                                  <  2:802829/124‑1 (MQ=255)
                                                                                     ctgctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt                                                                  >  1:802829/1‑124 (MQ=255)
                                                                                        ctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACAttacaga                                                                                                          <  2:633092/81‑6 (MQ=255)
                                                                                        ctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACAttacaga                                                                                                          >  1:633092/1‑76 (MQ=255)
                                                                                        ctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTaa                                                                                                         <  1:937749/82‑1 (MQ=255)
                                                                                        ctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTaa                                                                                                         >  2:937749/1‑82 (MQ=255)
                                                                                        ctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATg                                                        <  2:1114242/131‑1 (MQ=255)
                                                                                        ctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATg                                                        >  1:1114242/1‑131 (MQ=255)
                                                                                        ctgGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTg                                                >  2:210197/1‑139 (MQ=255)
                                                                                        ctgGAAATCTTTTTCCTGCTTTTTCCACTCGGCTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTg                                                >  2:447877/1‑139 (MQ=255)
                                                                                                   tttCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑c                                                                                                                                       >  1:568386/1‑41 (MQ=255)
                                                                                                   tttCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑c                                                                                                                                       <  2:568386/41‑1 (MQ=255)
                                                                                                      ccTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCa                                  <  1:698224/139‑1 (MQ=255)
                                                                                                         gCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGcaca                                                                                                                 <  1:826397/57‑1 (MQ=255)
                                                                                                         gCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑c                                                                                                                                       <  2:1413561/35‑1 (MQ=255)
                                                                                                         gCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑c                                                                                                                                       >  1:1413561/1‑35 (MQ=255)
                                                                                                         gCTTTTTCCACTCGGTTTGGATTGAGGATAGCAGC‑CCCCCCCAGG‑CTTCCCAGcaca                                                                                                                 >  2:826397/1‑57 (MQ=255)
                                                                                                          cTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGc                              <  1:447877/139‑1 (MQ=255)
                                                                                                          cTTTTTCCACTCGGTTTGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGc                              <  2:1175723/139‑1 (MQ=255)
                                                                                                                     cGGTTTGGATTGAGGATTGCAG‑‑CCCCCCCCGGCCTTCCCAGCCCTTTCTGTAATGGGTTACCGCCGC‑TTTCAGCACCCTTTTCCCGCCCCTTCCATTAATGCGGCCCTGTAAAATTCCCCCCATTGCCTGATTCACTaa                  >  2:283605/1‑139 (MQ=255)
                                                                                                                       gTTTGGATTGAGGATTGCAGCCCCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGATTCACTaa                  >  1:1026073/1‑139 (MQ=255)
                                                                                                                        tttGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTa                                              >  2:1427975/1‑109 (MQ=255)
                                                                                                                        tttGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTa                                              <  1:1427975/109‑1 (MQ=255)
                                                                                                                        tttGGATTGAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGATTCACTAAtt                >  1:1219661/1‑139 (MQ=255)
                                                                                                                                gAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCAt                                                             <  2:1046032/86‑1 (MQ=255)
                                                                                                                                gAGGATTGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCAt                                                             >  1:1046032/1‑86 (MQ=255)
                                                                                                                                      tGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATg                                                        <  2:174286/85‑1 (MQ=255)
                                                                                                                                      tGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATg                                                        >  1:174286/1‑85 (MQ=255)
                                                                                                                                      tGCAGC‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGATTCACTAATTGCTGGCCTTCGgcg  <  1:210197/139‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                       
AAATAGAGGATTATTTTAAATTCCCGACCAGGGCTTTGCGGCTATCTTCCAGAGTCACAACGCGGCTACAAACATCTTTGCCAAACTGCTGGAAATCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAG‑‑CCCCCCCAGG‑CTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCTGTAAAATTCCACCCATTGCCTGATTCACTAATTGCTGGCCTTCGGCG  >  NC_000913/3100894‑3101165

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A