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
A16 F57 I19 R4 125 90.3 3545000 95.6% 3389020 127.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP006881 3,725,237 A→G intergenic (‑69/‑460) U712_19205 ← / → U712_19210 Uncharacterized protein ywcI/Minor extracellular protease vpr

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,725,2370AG94.1% 148.7 / ‑5.7 53intergenic (‑69/‑460)U712_19205/U712_19210Uncharacterized protein ywcI/Minor extracellular protease vpr
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (33/15);  minor base C (0/3);  total (34/19)
Fisher's exact test for biased strand distribution p-value = 3.92e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑TTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAAC  >  CP006881/3725119‑3725353
                                                                                                                          |                                                                                                                    
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CGTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCCGCCCGCAAGAAAAGACGGCCGAtt                                                                                                   >  8:204652/1‑139 (MQ=255)
     caAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCCGCCGCCGCCCGCAAGAAAAGACGGCCGAtttcttt                                                                                              >  2:109393/1‑139 (MQ=255)
            atcacccACACCCTAAAAGATACAAGCAAACGTTTCATACAAAACCATCCCCCCGCTTCTTTTTGGCCGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCCGCCGCCGCCCGCAACAAACCACGGCCGATTTCTTTTCTCGCa                                                                                       <  6:218346/134‑1 (MQ=255)
              cATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGCAAAGACGGCCGATTTCTTTTGTCGCaaa                                                                                     >  4:390045/1‑139 (MQ=255)
               aTCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCTCAAGAAAAGACGGCCGATTTATTTTCTAGCaaa                                                                                     >  1:323732/1‑138 (MQ=255)
               aTCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCGTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCaaa                                                                                     >  5:345470/1‑138 (MQ=255)
                     acCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCCTTTTATAATCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTAGCAAAcaatccg                                                                              >  5:360080/1‑133 (MQ=255)
                          tAAAGATACAAGCAAACGTTTCATAGAAATACATCCCTCCGCTTCTTTTTGGCCGGCCGC‑CGTTTT‑T‑GCCGCCCGTTTTCTCAGCCGGCGCCCGCCAGAACAGCCGGCCGAGTTCTTTTGTGGCGAACTTGCGGgtc                                                                           >  6:145342/1‑137 (MQ=255)
                          tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCGGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGctc                                                                           >  3:212601/1‑137 (MQ=255)
                          tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTATCGGctc                                                                           >  8:309091/1‑137 (MQ=255)
                          tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGctc                                                                           >  4:216353/1‑137 (MQ=255)
                          tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCGTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCCGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACGTGCGGctg                                                                           >  6:345775/1‑136 (MQ=255)
                          tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTC‑TTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGAGTTCTTTTCTCGCAAACTAGCGGcaagag                                                                        >  8:211978/1‑134 (MQ=255)
                            accaaaCAAGCAACCGTTTAATAGAAAAACATCCCCCCGCCTTTTTTTGGCCGGCCGC‑CTTTTT‑A‑GCACCCCGTTTTCTCAGCCGCCCCCCGAAATAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAg                                                                        <  6:207140/133‑1 (MQ=255)
                             aGATACAACCAAACGTTTAATACAAAAACAACCCTCCGCTTCTTTTTGCCAGGCAGC‑CTTTTT‑A‑GCCGCCCGTTTTCTCCCCCCCCGCCCGCAAGAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa                                                                      <  1:77407/139‑1 (MQ=255)
                                 aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAAc                                                                  >  3:442356/1‑139 (MQ=255)
                                 aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGCTTTAATTTCTCGCAAACTAGCGGCGCTAGCAAAAc                                                                  >  3:391904/1‑139 (MQ=255)
                                 aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCGTTTCTCGCAAACTAGCGGCTCGAGCAAAAc                                                                  >  8:357360/1‑139 (MQ=255)
                                 aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTATTTTATCGCAAACTAGCGGCTCGAGCaaaa                                                                   >  3:125770/1‑138 (MQ=255)
                                 aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCCTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAAc                                                                  >  5:207140/1‑139 (MQ=255)
                                    aGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCa                                                               >  5:210324/1‑139 (MQ=255)
                                     gaaatcGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCGGGCAGC‑CTTTTT‑A‑GAAGCCGTTTTTCTCAGCCGCAGCCCGCAAGAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                              <  7:339710/134‑1 (MQ=255)
                                     gCAAACGTTTCATACAAAACCAGCCCTCCGCTTCTTTTTGCCGGGCAGCTT‑TTTT‑A‑GCCGCCGGTTTGCTCCGCCGCCCCCCGAAAAAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                              <  5:117326/139‑1 (MQ=255)
                                     gCAAACGTTTCATACAAAAACATCCCTCGCCTTCTTTTTGGCAGGCTGC‑G‑TTTTAA‑GCCGCCGGTTTGCTCACCCGCACCCCGAAATAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                              <  1:32964/139‑1 (MQ=255)
                                     ccacaCGTTTCATATAAAAACAACCCACCGCTGCTTTGGGCCCGGCACC‑CTTTTT‑C‑CCAGCCCGTTTGCACCCCCGCCCCCCCAATTAAACCACGGCCGATTTCTTTTCTCGCAAACTCGCGGCTCTAGCAAAACTCAt                                                              <  4:442356/135‑1 (MQ=255)
                                     ccAAACTTTTCAACCAAAACCATCCCTCCTCTTATTTTTGCCCGGCAGCTT‑TTTT‑C‑CCAGCCTTTTTTCACAGCCCCCGCCCTAAACAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                              <  6:218712/138‑1 (MQ=255)
                                     ccAAACTTTTATTAAAAAAAAACCCCTGGGTTTTTTTTTGGCCGGCCGCTT‑TTTT‑A‑CCCGCCGTTTTTCCCCGCCGCCGCCCCAAAAAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                              <  4:212601/138‑1 (MQ=255)
                                         cgttttCAAACAAAAACATCCCTCGGCTTGTTTTTGGCAGCCACC‑A‑TTTT‑ACGCCGCCTTTTTCCTCCGCCCCCCCCCGAAACAACACCCGGCCTATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                          <  8:409570/136‑1 (MQ=255)
                                         acttttCATAAAAAAACACCCCTCGGCTTTTTTTTGGCAGGCAGCGT‑TTTT‑C‑GCAGCCGGTTTTCTCACCCGCACCCCGAAACAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                          <  7:309091/136‑1 (MQ=255)
                                         accttacATACAAAAACAGCCCCCCGCTTATTTTGGGCCGCCAGC‑CTTTTT‑C‑CCCGCCGGTTTTATCCCCCGCAGCCCCCAAGAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                          <  5:322392/133‑1 (MQ=255)
                                         aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCCGCCGCAGCCCGCAAGAAACGACGGCCGAGTTCTTTTCTCGCAAACTAGCGGCTATAGCCAAACTCATgcat                                                          >  6:181476/1‑136 (MQ=255)
                                         aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                          >  7:144197/1‑139 (MQ=255)
                                         aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                          <  3:216353/139‑1 (MQ=255)
                                         aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTAGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                          >  5:218712/1‑139 (MQ=255)
                                         aCGTTCAATAGAAAAACACCCCGCCGCTTTTTTTGGGCCGGCCGC‑C‑TTTT‑ACCCCGCGCTTTTTACCAGCCGCCCCCGGCAATAAACCCCGGCCGATTTCTTTTCTCGCAAACAAGCGGCTCTAGCAAAACTCATGAct                                                          <  6:393164/139‑1 (MQ=255)
                                         aCGTTAAATATAAAAACATCCCTCCGTTTCTTTTTGGCAGGCAGCTT‑TTTT‑C‑CCAGCCGGTTTTCTCCGCCGCACCCCGAAAAAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                          <  3:305660/139‑1 (MQ=255)
                                                aTACAAAAACATCCCTCCGCTTATTTTTGGCCGTCTGCTT‑TTTT‑A‑GCAGCCCGTTTTCTCAGCCCCCGCCCGAAATAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGAt                                                   <  8:144197/139‑1 (MQ=255)
                                                     aaaaCATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGAcc                                              >  1:159412/1‑139 (MQ=255)
                                                         cATCCCTCCGCTTCTTTTTGGCTGGCACCAT‑TTTT‑A‑GCAGCCCGTTTCCTCCGCCGCACCCCGAAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTCGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTgg                                          <  6:178291/139‑1 (MQ=255)
                                                              cTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTAATGACTCTATGATAGACCGTGGaaa                                       >  8:419006/1‑137 (MQ=255)
                                                                 cGCTTCTTTTTGGCAGCCAGC‑CTTTTT‑C‑GCCGCCCGTTTGCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGaa                                  <  2:255141/139‑1 (MQ=255)
                                                                         tttGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTATTTTCTCGCAAACTATCGGCTCTAGCAAAACTCATGACTCTATGAAATACCGTGGAAAGAGAAATGttttt                          >  7:173431/1‑137 (MQ=255)
                                                                                ggcagC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCCGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAata                   >  7:4173/1‑139 (MQ=255)
                                                                                ggcagC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAata                   >  6:230570/1‑139 (MQ=255)
                                                                                 gcagC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa                                                                      >  2:131868/1‑87 (MQ=255)
                                                                                 gcagC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa                                                                      <  1:131868/87‑1 (MQ=255)
                                                                                                  agcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAAcc     >  4:304402/1‑138 (MQ=255)
                                                                                                  agcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAAATAGCGGCTCTAGCAAAACTCATGACTCTATGATAGCCCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAAca     >  3:188149/1‑137 (MQ=255)
                                                                                                   gcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCaa   >  7:285242/1‑139 (MQ=255)
                                                                                                    cccGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTGACAATATGAGTGAAAaaacaaac  >  8:180477/1‑139 (MQ=255)
                                                                                                    cccGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAccctgt  >  1:292896/1‑136 (MQ=255)
                                                                                                    cccGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTAGCAAACTAGCGGCTCTAGCAAAACTCCTGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCAAAATATGTGTGAAAAAACCAAc  >  5:381499/1‑139 (MQ=255)
                                                                                                      cGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCATTTCTCGCAAACTAGCGGCTCAAGCAAAACACAAGACTCTATGATACACCGTGGAAAGAGAATTATTTGTCACAATATGAGAGAAAAAACCAAc  >  5:153725/1‑137 (MQ=255)
                                                                                                                          |                                                                                                                    
TTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑TTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAAC  >  CP006881/3725119‑3725353

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A